Sirt4 activities

ABSTRACT

It has been discovered that Sirt4 possesses an ADP-ribosyltransferase activity. Sirt4 is localized to mitochondria, where it binds to and regulates the activity of proteins such as glutamate dehydrogenase. The ADP-ribosyltransferase activity of Sirt4 is important for the regulation of biological functions such as insulin secretion. Methods of screening for compounds that modulate the expression or activity of Sirt4 are provided. Also provided are methods of modulating insulin secretion, treating metabolic disorders, and treating neurodegenerative disorders by modulating the expression or activity of Sirt4.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority to U.S. application Ser. No.60/673,565, filed on Apr. 21, 2005, the contents of which areincorporated by reference in their entirety.

STATEMENT REGARDING FEDERALLY FUNDED RESEARCH

At least some of the work described herein was funded, in part, throughgrants from the National Institute of Health. The United Statesgovernment may, therefore, have certain rights in the invention.

SUMMARY

In one aspect, the disclosure features a method of evaluating Sirt4activity. The method includes providing a composition (e.g., a cell-freecomposition) that includes one or more of: a Sirt4 protein, anADP-ribosyl donor, and a substrate; and evaluating ADP-ribosylationactivity in the composition. The ADP-ribosyl donor can be NAD or an NADanalog, e.g., a labeled version of the donor, e.g., radio-labeledversions thereof, e.g., ³H, ¹⁴C, ³²P- or ³³P-labeled. ADP-ribosylationactivity can be evaluated by detecting a radiolabel associated with thesubstrate, e.g., NAD. ADP-ribosylation activity can be evaluated bydetecting the modification of the substrate or the ADP-ribosyl donor(e.g., NAD). The substrate can be separated from the composition priorto evaluation of ADP-ribosylation activity.

The substrate can include, e.g., glutamate dehydrogenase (GDH), aldehydedehydrogenase (ADH), adenine nucleotide transporter (ANT) or a homologthereof, or histones, or a fragment of any of the above. The substratecan be from a human or other mammal, e.g., a mouse, rat, pig, or cow. Inone embodiment, the substrate includes a peptide, e.g., a peptide from amitochondrial protein.

In one embodiment, the composition includes a test compound.

In one embodiment, the Sirt4 protein is at least 10% pure, e.g., 10%,20%, 30%, 40%, 50%, 75%, 80%, 90%, 95%, or 99% pure. The Sirt4 proteincan be expressed in recombinant cells and isolated therefrom. The Sirt4protein can be expressed in, e.g., E. coli cells, and isolatedtherefrom. The concentration of the Sirt4 protein in the composition canbe between 0.1 pM and 0.1 μM, e.g., between 0.1 pM and 10 pM, 10 pM and1 nM, or 1 nM and 0.1 μM.

In one embodiment, the Sirt4 protein can include the core domain ofSirt4 or other biologically active portion of full-length Sirt4. TheSirt4 protein can include the core domain of Sirt4, but not allsequences of a full-length Sirt4. Alternatively, the Sirt4 protein caninclude a full-length Sirt4. The Sirt4 protein can include a sequencethat is at least 85% identical, e.g., 85%, 90%, 95%, 98%, 99% identical,to SEQ ID NO:3 (an exemplary fragment of human Sirt4). The Sirt4 proteincan include a sequence at least 85% identical, e.g., 85%, 90%, 95%, 98%,99%, or 100% identical, to SEQ ID NO:1 (full-length human Sirt4) or caninclude one or more of a sequence at least 85% identical, e.g., 85%,90%, 95%, 98%, 99%, or 100% identical, to amino acid residues 29-314,29-308, 30-314, 36-308, 42-308, 42-300, or 36-314 of SEQ ID NO: 1. TheSirt4 protein can be human. The Sirt4 protein can include an artificialmutation, e.g., an alanine-scanned mutation.

In another aspect, this disclosure features a method of evaluating Sirt4activity in a cell. The method includes altering Sirt4 expression in anisolated cell and evaluating ADP-ribosylation activity associated withthe cell. Sirt4 expression can be decreased, e.g., by introducing to thecell a nucleic acid that decreases expression, e.g., an siRNA. Sirt4expression can be increased, e.g., by introducing to the cell a nucleicacid that encodes Sirt4 (e.g., a protein that includes a Sirt4 coredomain) operably linked to a promoter that drives expression of Sirt4.The isolated cell can include an exogenous nucleic acid that includes asequence encoding a Sirt4 protein. The isolated cell can be modified byintroduction of an exogenous promoter into an endogenous Sirt4 encodinggene. The cell can be, e.g., a yeast cell or a mammalian cell, e.g., apancreatic cell, brain cell, liver cell, adipose cell, muscle cell, skincell, or kidney cell.

In one embodiment, the method further includes comparing the activityevaluated in the presence of the test compound with the Sirt4 activityevaluated in the absence of the test compound. In one embodiment, themethod further includes evaluating the test compound in a cellular oranimal model of insulin secretion, diabetes, or a neurodegenerativedisorder, e.g., Alzheimer's disease.

In another aspect, this disclosure features a method of evaluating theeffect of a test compound on Sirt4. The method includes providing areaction mixture including a Sirt4 protein and a test compound, andevaluating an activity of Sirt4. In one embodiment, the activity ofSirt4 is an enzymatic activity, e.g., an ADP-ribosyltransferaseactivity. The reaction mixture can include NAD or an NAD analog. The NADor NAD analog can be radiolabeled, e.g., with ³H, ¹⁴C, ³²P or ³³P. Thereaction mixture can include an ADP-ribosylation substrate, e.g., GDH,aldehyde dehydrogenase (ADH), an adenine nucleotide transporter (ANT),or a histone.

In another embodiment, the activity of Sirt4 is a binding activity. Thebinding activity can be binding to the test compound or binding to aSirt4 binding partner, e.g., GDH, adenine nucleotide transporter 1 or 2(ANT), or insulin-degrading enzyme (IDE). The reaction mixture caninclude a Sirt4 binding partner, e.g., GDH, ANT, or IDE.

The test compound can be, e.g., a small molecule, a peptide, a protein,or an antibody. In one embodiment, the method is repeated for each of aplurality of test compounds from a chemical library.

In one embodiment, the Sirt4 protein is at least 10% pure, e.g., 10%,20%, 30%, 40%, 50%, 75%, 80%, 90%, 95%, or 99% pure. The Sirt4 proteincan be expressed in recombinant cells and isolated therefrom. The Sirt4protein can be expressed in, e.g., E. coli cells, and isolatedtherefrom. The concentration of the Sirt4 protein in the composition canbe between 0.1 pM and 0.1 μM, e.g., between 0.1 pM and 10 pM, 10 pM and1 nM, or 1 nM and 0.1 μM.

In one embodiment, the Sirt4 protein includes the core domain of Sirt4.The Sirt4 protein can include the core domain of Sirt4, but not allsequences of a full-length Sirt4. Alternatively, the Sirt4 protein caninclude a full-length Sirt4. The Sirt4 protein can include a sequencethat is at least 85% identical, e.g., 85%, 90%, 95%, 98%, 99% identical,to SEQ ID NO:3 (an exemplary fragment of human Sirt4). The Sirt4 proteincan include a sequence at least 85% identical, e.g., 85%, 90%, 95%, 98%,99% identical, to SEQ ID NO:1 (full-length human Sirt4) or amino acidresidues 29-314, 29-308, 30-314, 36-308, 42-308, 42-300, or 36-314 ofSEQ ID NO:1. The Sirt4 protein can be human. The Sirt4 protein caninclude an artificial mutation, e.g., an alanine scanned mutation. TheSirt4 protein can be a processed Sirt4 protein, e.g., a Sirt4 proteinthat lacks at least amino acids 1-14, 1-20, 1-27, or 1-28 of SEQ IDNO:1.

In one embodiment, the method further includes comparing the activityevaluated in the presence of the test compound with the Sirt4 activityevaluated in the absence of the test compound. In one embodiment, themethod further includes evaluating the test compound in a cellular oranimal model of insulin secretion, diabetes, or a neurodegenerativedisorder, e.g., Alzheimer's disease.

In another aspect, this disclosure features a method of identifying acompound that alters a Sirt4-associated parameter in a cell. The methodincludes contacting a test compound to a cell that expresses Sirt4, andevaluating a Sirt4-associated parameter associated with the cell. TheSirt4-associated parameter can be expression of Sirt4, e.g., measured aslevels of Sirt4 mRNA or protein. The Sirt4-associated parameter can beADP-ribosylation activity, e.g., measured as ADP-ribosylation of amitochondrial protein, e.g., GDH. The Sirt4-associated parameter can bebinding of Sirt4 to a protein, e.g., a mitochondrial protein, e.g., GDH,ANT, or IDE. The Sirt4-associated parameter can be the subcellularlocalization of Sirt4, e.g., measured by immunofluorescence microscopy.The Sirt4-associated parameter can be a parameter indicative ofmitochondrial function. The Sirt4-associated parameter can be theproteolytic modification state of Sirt4, e.g., an N-terminal proteolyticmodification. The Sirt4-associated parameter can be a level of a primaryor secondary metabolite.

The test compound can be, e.g., a small molecule, a peptide, a protein,or an antibody. In one embodiment, the method is repeated for each of aplurality of test compounds from a chemical library. The cell can be,e.g., a yeast cell or a mammalian cell, e.g., a pancreatic cell, braincell, liver cell, adipose cell, muscle cell, skin cell, or kidney cell.A peptide is generally a polymer of less than 24 amino acids in length.Exemplary peptides include peptides between 3-24, 3-20, 3-12, 3-8, or5-12 amino acids in length.

In one embodiment, the method further includes comparing the parameterevaluated in the presence of the test compound with the Sirt4-associatedparameter evaluated in the absence of the test compound. In oneembodiment, the method further includes evaluating the test compound ina cellular or animal model of insulin secretion, diabetes, or aneurodegenerative disorder, e.g., Alzheimer's disease, Parkinson'sdisease, or Huntington's disease or other neurological disorder.

In another aspect, this disclosure features a method of modulatinginsulin secretion in response to glucose. The method includes modulatingthe expression or activity of Sirt4 in an insulin-secreting cell.Insulin secretion can be increased, e.g., by decreasing the expressionor activity of Sirt4. Insulin secretion can be decreased, e.g., byincreasing the expression or activity of Sirt4. Insulin secretion can bemodulated in vitro, e.g., in a cultured cell or tissue explant. Insulinsecretion can be modulated in a subject, e.g., a mammal, e.g., a human,by administering an agent that modulates Sirt4 expression or activity.

In another aspect, this disclosure features an isolated cell includingan RNA (e.g., a dsRNA, anti-sense RNA, or siRNA) that inhibits theexpression of Sirt4. The cell can be a pancreatic cell, e.g., apancreatic β-cell. The cell can be an insulin-secreting cell.

In another aspect, this disclosure features a method of treating orpreventing diabetes or a diabetes-related disorder (e.g., pre-diabetes)by administering to a subject an agent that decreases the expression oractivity of Sirt4 in an amount effective to treat or prevent diabetes orthe diabetes-related disorder. The agent can be an agent identified byany of the screening methods described herein.

In another aspect, this disclosure features a method of treating orpreventing a disorder, e.g., a metabolic disorder. The method includesadministering to a subject an agent that modulates the expression oractivity of Sirt4 in an amount effective to treat or prevent thedisorder, e.g., the metabolic disorder. The metabolic disorder can be,e.g., diabetes, insulin resistance, metabolic syndrome (syndrome X),obesity, or pre-diabetes. The expression or activity of Sirt4 can bemodulated in an insulin-secreting cell, e.g., a pancreatic β-cell. Inone embodiment, the expression or activity of Sirt4 is decreased, thusincreasing insulin secretion. In one embodiment, the expression oractivity of Sirt4 is increased, thus decreasing insulin secretion. Theagent can be an antagonistic nucleic acid that reduces Sirt4 expression,e.g., an siRNA that targets Sirt4.

A related method includes providing a composition that includes an agentthat modulates expression or activity of Sirt4, evaluating an aliquot ofthe composition (e.g., using a method described herein), e.g., forability of the aliquot to modulate expression or activity of Sirt4, andadministering to a subject an agent that modulates the expression oractivity of Sirt4 in an amount effective to treat or prevent thedisorder, e.g., the metabolic disorder, or diabetes.

In another aspect, this disclosure features a method of treating orpreventing a symptom of a neurodegenerative disorder, e.g., Alzheimer'sdisease, Parkinson's disease, or Huntington's disease, or otherneurological disorder. The method includes administering to a subject acompound that increases the expression or activity of Sirt4 in an amounteffective to treat or prevent the neurodegenerative disorder. Theneurodegenerative disorder can be one, e.g., that involves accumulationof β-amyloid peptide.

In another aspect, this disclosure features a method that includesevaluating a Sirt4-associated parameter in a pancreatic cell, braincell, or other Sirt4-expressing cell. The Sirt4-associated parameter canbe an indicator of expression of Sirt4, levels of Sirt4 mRNA or protein,or ADP-ribosylation activity by Sirt4 protein. The Sirt4-associatedparameter can be an indicator of ADP-ribosylation of a mitochondrialprotein, e.g., GDH. The Sirt4-associated parameter can be an indicatorof binding of Sirt4 to a Sirt4 binding partner, e.g., a mitochondrialprotein, e.g., GDH, ANT, or IDE. For example, the Sirt4 binding partneris a human protein.

In another aspect, this disclosure features a method that includesevaluating a Sirt4-associated parameter in mitochondria, e.g., isolatedmitochondria. The Sirt4-associated parameter can be an indicator oflevels of Sirt4 protein, or ADP-ribosylation activity by Sirt4 protein.The Sirt4-associated parameter can be an indicator of ADP-ribosylationof a mitochondrial protein, e.g., GDH. The Sirt4-associated parametercan be an indicator of binding of Sirt4 to a Sirt4 binding partner,e.g., GDH, ANT, or IDE. The Sirt4-associated parameter can bemitochondrial function.

In another aspect, this disclosure features a method that includesevaluating the ADP-ribosylation state of glutamate dehydrogenase in apancreatic cell, brain cell, or other Sirt4-expressing cell. The cellscan include human cells.

In another aspect, this disclosure features an antibody that binds toSirt4, e.g., human Sirt4, and distinguishes between mature, processedSirt4, e.g., human Sirt4, and unprocessed Sirt4, e.g., human Sirt4. Theantibody can bind preferentially to mature, processed Sirt4, relative tounprocessed Sirt4. For example, the antibody binds to amino acidresidues 29-32 of a Sirt4 whose N-terminus begins at a residuecorresponding to residue 29 of SEQ ID NO:1. The antibody can bindpreferentially to unprocessed Sirt4, relative to mature, processedSirt4. For example, the antibody binds to an epitope within amino acidresidues 1-28 of SEQ ID NO:1.

In another aspect, this disclosure features a method that includesprocessing state of Sirt4, e.g., in the N-terminal region, e.g., todetermine if one or more amino acids from amino acid residues 1-28 ofSEQ ID NO:1 are present or absent. The method can be used to evaluate asample that includes Sirt4. The sample can include, or contain, e.g., acell, a cell-free extract, or mitochondria, e.g., isolated mitochondria.The method can include determining the N-terminal sequence of Sirt4, thesequence of one or more amino acids in the N-terminal 20% of theprotein, or the size of peptide fragments of Sirt4 (e.g., using massspectroscopy and optionally proteolysis). The method can includecontacting the sample to an antibody that binds to Sirt4, e.g., humanSirt4, and distinguishes between mature, processed Sirt4, e.g., humanSirt4, and unprocessed Sirt4, e.g., human Sirt4. The sample can includea pancreatic cell, brain cell, or other Sirt4-expressing cell. Thesample can include human cells.

In another aspect, this disclosure features a method of directingexpression of a target sequence to an insulin-producing cell. The methodincludes providing a pancreatic cell that contains a nucleic acid thatincludes regulatory sequences from the SIRT4 gene operably linked to atarget sequence for expression, wherein the target sequence is not asequence from the Sirt4 gene. The target sequence can encode a protein,e.g., insulin or another secreted protein. The target sequence canencode an anti-sense nucleic acid.

In another aspect, this disclosure features a method of isolating aSirt4 protein. The method includes isolating mitochondria from a cellthat expresses a Sirt4 protein and separating the Sirt4 from at leastone other mitochondrial protein. The Sirt4 protein can beproteolytically processed. The cell can be a human cell.

In another aspect, this disclosure features a method of isolating aSirt4 protein. The method includes isolating mitochondria from a cellthat expresses a Sirt4 protein and separating the Sirt4 from at leastone other mitochondrial protein. The Sirt4 protein can beproteolytically processed.

In another aspect, this disclosure features a kit including a Sirt4protein and an ADP-ribosylation substrate, e.g., GDH. The kit canfurther include an ADP-ribosyl donor, e.g., NAD or an NAD analog.

In one aspect, the invention features a method that includes genotypinga human gene that encodes a sirtuin, e.g., SIRT4 or another SIRT4 andrecording information about the genotype in association with informationabout a metabolic disorder, e.g., diabetes, pre-diabetes, orhyperinsulinemia, or other disorder described herein (including, e.g.,neurological disorders).

The invention also features a method that includes genotyping a humangene that encodes a sirtuin, e.g., SIRT4 or another SIRT4 and recordinginformation about the genotype in association with information about ametabolic disorder or other disorder described herein.

In one aspect, the invention features a method that includes a)determining the identity of at least one nucleotide in the SIRT4 locuson human chromosome 12q of a subject; and b) creating a record whichincludes information about the identity of the nucleotide andinformation relating to a metabolic disorder, e.g., diabetes, or otherdisorder described herein, e.g., a disorder-related parameter of thesubject, wherein the a metabolic disorder (e.g., diabetes, or otherdisorder described herein) is other than the genotype of a nucleotide inthe 12q region. The method can be used, e.g., for gathering geneticinformation.

In one embodiment, the determining includes evaluating a sampleincluding human genetic material from the subject.

Another method includes: a) evaluating a parameter of a SIRT4 moleculefrom a mammalian subject; b) evaluating a parameter associated with ametabolic disorder, e.g., diabetes, or other disorder described hereinof the subject wherein the parameter is other than a parameter of aSIRT4 molecule; and c) recording information about the SIRT4 parameterand information about the parameter, wherein the information about theparameter and information about the phenotypic trait are associated witheach other in the database. For example, the parameter is a phenotypictrait of the subject.

In one embodiment, the SIRT4 molecule is a polypeptide and the SIRT4parameter includes information about a SIRT4 polypeptide. In anotherembodiment, the SIRT4 molecule is a nucleic acid and the SIRT4 parameterincludes information about identity of a nucleotide in the SIRT4 gene.

In an embodiment, the subject is an embryo, blastocyst, or fetus. Inanother embodiment, the subject is a post-natal human, e.g., a child oran adult (e.g., at least 20, 30, 40, 50, 60, 70 years of age).

In one embodiment, step b) is performed before or concurrent with stepa). In one embodiment, the human genetic material includes DNA and/orRNA.

The method can further include comparing the SIRT4 parameter toreference information, e.g., information about a correspondingnucleotide from a reference sequence. For example, the referencesequence is from a reference subject , e.g., a subject who has a commonallele, especially one who is homozygous for a common allele. In anotherembodiment, the reference sequence is from a reference subject that hasa metabolic disorder, e.g., diabetes, e.g., early or late-onsetdiabetes, or other disorder described herein.

In one embodiment, the method further includes comparing the nucleotideto a corresponding nucleotide from a genetic relative or family member(e.g., a parent, grandparent, sibling, progeny, prospective spouse,etc.).

In one embodiment, the method further includes evaluating risk ordetermining diagnosis of a metabolic disorder, e.g., diabetes, or otherdisorder described herein in the subject as a function of the genotype.

In one embodiment, the method further includes recording informationabout the SIRT4 parameter and parameter, e.g., in a database. Forexample, the information is recorded in linked fields of a database(e.g., SIRT4 parameter is linked to at least one of: corresponding SIRT4parameter and/or data regarding comparison with the reference sequence).The nucleotide can be located in an exon, intron, or regulatory regionof the SIRT4 gene. For example, the nucleotide is a SNP. The identity ofat least one SNP from Table 1 can be evaluated. In one embodiment, aplurality of nucleotides (e.g., at least 10, 20, 50, 100, 500, or 1000nucleotides are evaluated (e.g., consecutive or non-consecutive)) in theSIRT4 locus are evaluated. In another embodiment, a single nucleotide isevaluated.

In one embodiment, the method includes one or more of: evaluating anucleotide position in the SIRT4 locus on both chromosomes of thesubject; recording the information (e.g., as phased or unphasedinformation); aligning the genotyped nucleotides of the sample and thereference sequence; and identifying nucleotides that differ between thesubject nucleotides and the reference sequence.

The method can be repeated for a plurality of subjects (e.g., at least10, 25, 50, 100, 250, 500 subjects).

In one embodiment, the method can include comparing the information ofstep a) and step b) to information in a database, and evaluating theassociation of the genotyped nucleotide(s) with a metabolic disorder,e.g., diabetes, or other disorder described herein.

In another aspect, the disclosure features a protein, e.g., an isolatedprotein, that includes a Sirt4 core domain, but that does not includeall or part of the Sirt4 leader sequence. For example, the protein canbe lacking at least amino acids that correspond to 1-14, 1-20, 1-26,1-27, or 1-28 of SEQ ID NO:1, e.g., such amino acids of SEQ ID NO:1itself. The protein may include another amino acid or another amino acidsequence, e.g., amino terminal to the remaining region of SIRT4. Forexample, there may be a methionine immediately amino terminal to residue29 of SEQ ID NO:1, a tag sequence, or a heterologous leader sequence.

The protein can be recombinantly produced, e.g., from E. coli. Theprotein can be provided in a preparation that is substantially free ofmitochondrial proteins. In some embodiments, the preparation includesone, but not more than five species of mitochondrial proteins.

An “isolated” or “purified” polypeptide or protein is separated from atleast some cellular material or other contaminating proteins from thecell or tissue source from which the protein is derived, orsubstantially free from chemical precursors or other chemicals whenchemically synthesized. An isolated protein can be substantially free ofcontaminating materials. “Substantially free” means that the protein ofinterest in the preparation is at least 10% pure. In an embodiment, thepreparation of the protein has less than about 30%, 20%, 10% and morepreferably 5% (by dry weight), of a contaminating component (e.g., aprotein not of interest, chemical precursors, and so forth). When theprotein or biologically active portion thereof is recombinantlyproduced, it is also preferably separated from culture medium, e.g.,culture medium represents less than about 20%, more preferably less thanabout 10%, and most preferably less than about 5% of the volume of theprotein preparation. Exemplary preparations of proteins described hereininclude isolated or purified preparations of at least 0.01, 0.1, 1.0,and 10 milligrams in dry weight.

A “non-essential” amino acid residue is a residue that can be alteredfrom the wild-type sequence of protein without abolishing orsubstantially altering activity, e.g., the activity is at least 20%,40%, 60%, 70%, or 80% of wild-type. An “essential” amino acid residue isa residue that, when altered from the wild-type sequence results inabolishing activity such that less than 20% of the wild-type activity ispresent. Conserved amino acid residues are frequently predicted to beparticularly unamenable to alteration.

A “conservative amino acid substitution” is one in which the amino acidresidue is replaced with an amino acid residue having a similar sidechain. Families of amino acid residues having similar side chains havebeen defined in the art. These families include amino acids with basicside chains (e.g., lysine, arginine, histidine), acidic side chains(e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g.,glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine),nonpolar side chains (e.g., alanine, valine, leucine, isoleucine,proline, phenylalanine, methionine, tryptophan), beta-branched sidechains (e.g., threonine, valine, isoleucine) and aromatic side chains(e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, apredicted nonessential amino acid residue in a protein is preferablyreplaced with another amino acid residue from the same side chainfamily. Alternatively, in another embodiment, mutations can beintroduced randomly along all or part of a coding sequence, such as bysaturation mutagenesis, and the resultant mutants can be screened forbiological activity to identify mutants that retain activity. Followingmutagenesis, the encoded protein can be expressed recombinantly and theactivity of the protein can be determined.

As used herein, a “biologically active portion” of a protein includes afragment of a protein of interest, e.g., a target protein, whichparticipates in an interaction, e.g., an intramolecular or aninter-molecular interaction, e.g., a binding or catalytic interaction.An inter-molecular interaction can be a specific binding interaction oran enzymatic interaction (e.g., the interaction can be transient and acovalent bond is formed or broken). An inter-molecular interaction canbe between the protein and another protein, between the protein andanother compound, or between a first molecule and a second molecule ofthe protein (e.g., a dimerization interaction). Biologically activeportions of a protein include peptides comprising amino acid sequencessufficiently homologous to or derived from the amino acid sequence ofthe protein which include fewer amino acids than the full length,natural protein, and exhibit at least one activity of the naturalprotein.

Biologically active portions can be identified by a variety oftechniques including truncation analysis, site-directed mutagenesis, andproteolysis. Mutants or proteolytic fragments can be assayed foractivity by an appropriate biochemical or biological (e.g., genetic)assay. In some embodiments, a biologically active portion is folded,e.g., the portion includes one or more folded domains, e.g.,independently folded domains.

Exemplary biologically active portions can include at least a minimalenzymatic core domain that has an active site and detectable enzymaticactivity in vitro.

Exemplary biologically active portions include between 5-100% of aprotein, e.g., between 10-99, 10-95, 15-94, 15-90, 20-90, 25-80, 25-70,25-60, 25-50, 25-40, 5-25, or 75-90% of the protein, e.g. a targetprotein. Biologically active portions can include, e.g., internaldeletions, insertions (e.g., of a heterologous sequence), terminaldeletions, and substitutions (e.g., conservative substitutions).Typically, biologically active portions comprise a domain or motif withat least one activity of the protein.

The terms “modulated” and “differentially regulated” include increasing(including, for example, activation or stimulation) and decreasing(including, for example, inhibition or suppression) relative to areference level.

The details of one or more embodiments are set forth in the accompanyingdrawings and the description below. Other features, objects, andadvantages of the invention will be apparent from the description anddrawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1. Sirt4 is an ADP-ribosyltransferase. FIG. 1A. 293T cells weretransiently transfected with pCMV-FLAG-4A® (control), phSirt4FLAG orhSirt4. Protein expression was verified by anti-FLAG, or anti-hSirt4antibodies. FIG. 1B. hSirt4-FLAG or hSirt1-FLAG was immunoprecipitatedfrom 293T cells and dialyzed to remove FLAG peptide. 50 ng of eachprotein was assayed for deacetylase activity after a 1 hour at 37° C.incubation with the FLUOR DE LYS™ substrate (BIOMOL) in the absence(open bars) or presence (black bars) of 1 mM NAD⁺. FIG. 1C.ADP-ribosyltransferase activity of hSirt4-FLAG, hSirt5-FLAG or buffercontrol was assessed. 50 ng of protein was incubated with [³²P]-NAD⁺ inthe presence of core histone proteins as the substrate. Experiments werealso performed in the presence of 1 mM nicotinamide. FIG. 1D. Massspectrometry was used to analyze histone 2A protein that was incubatedfor 30 min at 37° C. in the presence of 1 mM NAD⁺with or without Sirt4.

FIG. 2. Sirt4 localizes to mitochondria in human and mouse cells. FIG.2A. HepG2 cells were co-transfected with phSirt4-GFP (green),pDS-RED-MITO (red) or pGFP alone (FIG. 2B. green), and the fluorescencewas visualized after 48 h using a confocal microscope. FIG. 2C. MIN6cells were disrupted by homogenization and the mitochondrial fractionwas isolated by sucrose centrifugation. Mitochondrial enrichment in thefinal sample was assessed by anti-HSP60 antibody. Endogenous Sirt4 wasdetected by anti-mSirt4 antibody. FIG. 2D. N-terminal sequences forhSirt3 and hSirt4 are shown, and their potential cleavage sites areindicated by arrows.

FIG. 3. Sirt4 is abundant in pancreatic islets. Sections of mousepancreas were assessed for Sirt4 expression by anti-mSirt4 antibodies(red), and β-cells were identified by using antibodies against insulin(green). Samples were visualized at 10× (FIG. 3A) or 40× (FIG. 3B)magnification.

FIG. 4. The role of Sirt4 in insulin secretion. FIG. 4A. The levels ofSirt4 were reduced in MIN6 cells infected with virus that containedSirt4 RNAi sequences compared to cells infected with pSUPER. FIG. 4B.Insulin secretion was measured from control or RNAi MIN6 cells. Cellswere pre-incubated with KRB buffer containing 3 mM glucose, then cellswere shifted to buffer containing either 3 mM (open bars) or 16.7 mMglucose (filled bars). Insulin in the buffer was measured by ELISA aftera 45 min incubation at 37° C. FIG. 4C. Insulin remaining inside cellswas measured at the end of the insulin secretion assays by ELISA.

FIG. 5. Glutamate dehydrogenase is ADP-ribosylated in vivo and interactswith Sirt4. FIG. 5A. Mitochondria (50 mg) from 293T cells were incubatedwith [³²P]-NAD at 37° C. for 30 min. Proteins were separated bySDS-PAGE, transferred to a nitrocellulose membrane, and radioactivitywas measured by exposure to film. FIG. 5B. Mitochondrial proteins wereADP-ribosylated as described for FIG. 5A, and lysis was performed inNP-40 buffer containing 10 mM DTT and 0.5 mM EDTA. Clarified lysate wasincubated with protein A resin that had been pre-incubated withantibodies against hSirt4, ANT or glutamate dehydrogenase (GDH). FIG.5C. 293T cells were transiently transfected with 10 μg of pCMV (V) orphSirt4-FLAG (4). Cells were harvested and lysed in NP-40 buffercontaining protease inhibitors and 1 mM DTT. The clarified lysate wasincubated for 2 h at 4° C., while rotating, with resin that had beenpre-incubated with antibodies for Gal4, FLAG, hSirt4, or GDH. The resinwas washed six times with lysis buffer and protein complexes weresubjected to western blot analysis using antibodies against FLAG or GDH.FIG. 5D. An endogenous interaction between Sirt4 and glutamatedehydrogenase was determined in MIN6 cells. 5-10 cm plates of MIN6 cellswere harvested and lysed as described above. Lysates were incubated withresin pre-incubated with antibodies for mSirt4 or Gal4. Proteincomplexes were subjected to western blot analysis using antibodies formSirt4 or GDH. FIG. 5E. The effect of Sirt4 overexpression on glutamatedehydrogenase ADP-ribosylation was investigated in 293T cells that weretransiently transfected with hSirt4-FLAG. Mitochondria were labeled with[³²P]-NAD, and then proteins were immunoprecipitated using antibodiesagainst FLAG or GDH. Proteins were separated by SDS-PAGE, transferred tonitrocellulose membrane, and the radioactivity was measured by exposureto x-ray film.

FIG. 6. Glutamate dehydrogenase inhibition by Sirt4. FIG. 6A. Theenzymatic activity of glutamate dehydrogenase (50 mg in 200 ml) wasmeasured before (open bars, T=0) after a 60 min incubation (filled bars,T=60) at 37° C. with hSirt4-FLAG (50 ng) or a buffer control in thepresence of 1 mM NAD⁺. Experiments were replicated 3-5 times. FIG. 6B.Inhibition of glutamate dehydrogenase by Sirt4 requires 1 mM NAD⁺.Glutamate dehydrogenase (50 mg) was incubated with Sirt4 at 37° C. inthe presence (pink) or absence (blue) of I mM NAD+. Aliquots (1 ml) wereremoved at T=0, 5, 15, 30, 60, or 120 min, and glutamate dehydrogenaseactivity was measured for each time point. FIG. 6C. The activity ofglutamate dehydrogenase was measure in mitochondrial lysates (30 mg)from control or Sirt4 RNAi cells. Experiments were performed 3-5 timesusing cell lines from two separate infections.

FIG. 7. Elevated glutamate dehydrogenase activity contributes toincreased insulin secretion in Sirt4 RNAi cells. FIG. 7A. MIN6 cellswere co-infected with RNAi for Sirt4 and glutamate dehydrogenase, andprotein levels were compared to control infections. FIG. 7B. Insulinsecretion assays were performed in double-infected or control cells asdescribed previously. FIG. 7C. Insulin secretion assays were performedin control or Sirt4 RNAi treated cells in the presence or absence ofBCH, an activator of glutamate dehydrogenase.

FIG. 8. ATP and respiration in Sirt4 RNAi treated cells. FIG. 8A. Totalcellular ATP was measured in 20,000 control or Sirt4 RNAi MIN6 cells.ATP was measure after incubation in 3 (open bars) or 16.7 mM (filledbars) glucose as described for insulin secretion assays. FIG. 8B. Oxygenconsumption was measured using a Clark electrode in control or Sirt4RNAi treated cells that were incubated in 16.7 mM glucose.

FIG. 9 is a graphical overview of conserved putative transcriptionfactor binding sites in the region 5 kb upstream of human and mouseSirt4 as determined using the rVISTA program. Tick marks representconserved binding sites. Predicted transcription factors are indicatedon the left. Percent identity between the sequences is indicated on thebottom graph.

DETAILED DESCRIPTION

Sirt4 is a mitochondrial protein. It interacts with glutamatedehydrogenase, insulin degrading enzyme and an adenine nucleotidetransporter, and can regulate insulin secretion. Agents that modulatethe expression or activity of Sirt4, e.g., agents described herein oridentified by the methods described herein, can be useful in treating orpreventing metabolic disorders, e.g., the metabolic syndrome, obesity,elevated cholesterol, or diabetes (e.g., type 1 diabetes mellitus ortype 2 diabetes mellitus); and neurodegenerative disorders, e.g.,Alzheimer's disease, as well as other disorders.

Sirt4 Proteins

The Sirt4 proteins belong to the sirtuin family, proteins identified assharing significant sequence identity to Saccharomyces cerevisiae SIR2.

As used herein, the term “Sirt4” or “Sirt4 protein” refers to proteins,e.g., eukaryotic proteins, e.g., mammalian proteins, comprising aconserved core domain classified in the Conserved Domain Database groupcd01049 (SIRT4) (Marchler-Bauer et al. (2005) Nucleic Acids Res. 33:D192-6), functional domains, fragments (e.g., functional fragments),e.g., fragments of at least 8 amino acids, e.g., at least 8, 18, 28, 64,128, 150, 180, 200, 220, 240, 260, or 280 amino acids, and variantsthereof. Exemplary Sirt4 proteins include those designated GenBankNP_(—)036372 (human Sirt4) and Q8R216 (mouse Sirt4). Homologs of Sirt4proteins will share 60%, 80%, 85%, 90%, 95%, 98%, 99% sequence identityto a known Sirt4 protein and, e.g., feature ADP-ribosyltransferaseactivity. Eukaryotic Sirt4 proteins may be localized, e.g., tomitochondria.

An exemplary human Sirt4 sequence (NP_(—)036372) is as follows: (SEQ IDNO:1) MKMSFALTFRSAKGRWIANPSQPCSKASIGLFVPASPPLDPEKVKELQRFITLSKRLLVMTGAGISTESGIPDYRSEKVGLYARTDRRPIQHGDFVRSAPIRQRYWARNFVGWPQFSSHQPNPAHWALSTWEKLGKLYWLVTQNVDALHTKAGSRRLTELHGCMDRVLCLDCGEQTPRGVLQERFQVLNPTWSAEAHGLAPDGDVFLSEEQVRSFQVPTCVQCGGHLKPDVVFFGDTVNPDKVDFVHKRVKEADSLLVVGSSLQVYSGYRFILTAWEKKLPIAILNIGPTRSDD LACLKLNSRCGELLPLIDPC

An exemplary mouse Sirt4 sequence (Q8R216) is as follows: (SEQ ID NO:2)MSGLTFRPTKGRWITHLSRPRSCGPSGLFVPPSPPLDPEKIKELQRFISLSKKLLVMTGAGISTESSIPDYRSEKVGLYARTDRRPIQHIDFVRSAPVRQRYWARNFVGWPQFSSHQPNPAHWALSNWERLGKLHWLVTQNVDALHSKAGSQRLTELHGCMHRVLCLNCGEQTARRVLQERFQALNPSWSAEAQGVAPDGDVFLTEEQVRSFQVPCCDRCGGPLKPDVVFFGDTVNPDKVDFVHRRVKEADSLLVVGSSLQVYSGYRFILTAREQKLPIAILNIGPTRSDDLACLKLDSRCGELLPLIDPRRQHSDVQRLEMNFPLSSAAQDP

Sirt4 is post-translationally processed to form mature Sirt4 by cleavageof the N-terminus after serine 28 of SEQ ID NO:1 (underlined). TheN-terminus of SEQ ID NO:2 is predicted to be similarly cleaved(underlined).

The conserved Sirt4 core domain of human Sirt4 (SEQ ID NO:3) includesabout amino acids 47-308 of SEQ ID NO:1. That of murine Sirt4 includesabout amino acids 44-305 of SEQ ID NO:2. Other exemplary fragments ofhuman Sirt4 include: 29-314, 29-308, 30-314, 36-308, 42-308, 42-300, and56-314. Human and mouse Sirt4 share about 89% sequence identity withinthis conserved core domain. It is also possible to make chimericproteins that include one or more segments from human Sirt4 and one ormore segments from mouse Sirt4. Such chimeras, for example, will includea number of proteins that are between 89% to 100% identical to human ormouse Sirt4.

Some simple examples include proteins that have an N-terminal half fromone of the two species and a C-terminal half from the other. The switchover point can be located at an amino acid residue between about 5-10,10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, or 90-95% of thelength of human Sirt4.

A fragment of full length Sirt4 can have at least one function of Sirt4protein and/or be folded. Functional fragments can, for example, haveADP-ribosyltransferase activity and/or ability to interact with a Sirt4binding partner, e.g., glutamate dehydrogenase (GDH), adenine nucleotidetransporter 1 or 2 (ANT), or insulin-degrading enzyme (IDE).

Variants of Sirt4 proteins can be produced by standard means, includingsite-directed and random mutagenesis. Preferably, amino acid 61 is athreonine, amino acid 70 is a glycine, amino acid 71 is an isoleucine,amino acid 144 is an asparagine, or amino acid 146 is an aspartic acid.

Assays

This disclosure includes methods for evaluating Sirt4, including Sirt4enzymatic activity. One general category of methods includingevaluating, directly or indirectly, ADP ribosylation activity of a Sirt4protein. The protein can be a full length Sirt4 protein, a fragmentthereof, or other variant thereof.

Detection of ADP ribosylation activity can be used to evaluateartificial or naturally occurring variants of a Sirt4 protein. In afirst exemplary implementation, a Sirt4 genomic nucleic acid or mRNA(e.g., as cDNA) is amplified from a subject (e.g., a human subject.Protein encoded by the nucleic acid is evaluate for ADP ribosylationactivity. In a second exemplary implementation,. a Sirt4 gene issubjected to artificial mutagenesis to produce varied nucleic acids. Oneor more Sirt4 proteins encoded by such nucleic acids are evaluated forADP ribosylation activity. Examples of artificial mutagenesis includerandom point mutagenesis, site-directed mutagenesis (e.g., alaninescanning), DNA shuffling, and partial exonuclease treatment.

It is also possible to evaluate Sirt4 activity in the presence of a testcompound or test condition. The method can be used to screen acollection of compounds, e.g., a chemical library of small molecules.The method can also be used to evaluate a single compound, e.g., aquality control step, e.g., for a pharmaceutical or other product.

One exemplary method includes providing a reaction mixture that includesSirt4 and a test compound, and evaluating an activity of Sirt4. Anotherexemplary method includes contacting a test compound to a cell thatexpresses Sirt4 and evaluating a Sirt4 parameter, e.g., expression oractivity, in the cell. In some embodiments, in initial rounds ofscreening, it is possible to use mixtures (e.g., pools) of differentcompounds.

The activity of Sirt4 can be assayed, e.g., in the presence of acompound.

Exemplary “Sirt4 activities” include ADP-ribosyltransferase function(e.g., ability to ADP-ribosylate a substrate, e.g., glutamatedehydrogenase, aldehyde dehydrogenase, or a histone); and interactionwith a Sirt4 binding partner, e.g., physical association with a Sirt4binding partner such as glutamate dehydrogenase (GDH), insulin degradingenzyme (IDE), or adenine nucleotide translocase (ANT), or fragmentsthereof.

In one aspect, the effect of a test compound on Sirt4 activity isevaluated by providing a reaction mixture that includes Sirt4 and thetest compound, and evaluating an activity of Sirt4. The reaction mixturecan include nicotinamide adenine nucleotide (NAD) or an NAD-likecompound, e.g., comprising a radioactive isotope, e.g., ³²p, ³³P, ¹⁴C,³H. An “NAD-like compound” refers to a compound (e.g., a synthetic ornaturally occurring chemical, drug, protein, peptide, small organicmolecule) that possesses structural similarity to component groups ofNAD (e.g., adenine, ribose and phosphate groups) or functionalsimilarity (e.g., oxidation of substrates, supports ADP-ribosylation ofa histone in the presence of Sir2). For example, NAD-like compounds canbe NADH, NADP, NADPH, 3-aminobenzamide or 1,3-dihydroisoquinoline(Vaziri et al. (1997) EMBO J. 16:6018-6033), nicotinamide,iso-nicotinamide, non-hydrolyzable NAD, biotinylated NAD, andfluorescent analogs of NAD (e.g., 1,N6-ethenoNAD).

A parameter associated with Sirt4 can be evaluated, e.g., in thepresence or absence of a test compound. Exemplary Sirt4-associatedparameters include transcription of Sirt4 mRNA, levels of Sirt4 mRNA,levels of Sirt4 protein, ADP-ribosylation activity of Sirt4, levels ofADP-ribosylation of mitochondrial proteins (e.g., glutamatedehydrogenase), activity of Sirt4-regulated proteins (e.g., glutamatedehydrogenase activity, measured by monitoring NADH absorption at 340nm), binding of Sirt4 to Sirt4-binding partners (e.g., GDH, ANT, andIDE), bound vs. unbound state of Sirt4-associated proteins, andmitochondrial function, monitored by measuring respiration and ATPproduction. Other parameters that can be evaluated include qualitativeor quantitative measures of insulin secretion, insulin levels, β-amyloidlevels, β-amyloid degradation activity, or levels of other biomoleculesincluding primary and secondary metabolites, e.g., small molecules,carbohydrates (e.g., glucose), peptides, lipids, or lipoproteins (e.g.,low density lipoproteins, high density lipoproteins). The primary andsecondary metabolites assayed can be endogenous, or as a result of theadministration of a compound. Sirt4-associated parameters can beevaluated singly or in combination, e.g., to form a profile.

The assays described herein can also be adapted for other sirtuinproteins, e.g., sirtuins other than Sirt4.

Proteins described herein can be made by recombinant or other methods.See, e.g., techniques described in Sambrook & Russell, MolecularCloning: A Laboratory Manual, 3rd Edition, Cold Spring HarborLaboratory, N.Y. (2001). The proteins can be purified, e.g., usingpurification tags and other standard methods. See, e.g., techniquesdescribed in Scopes (1994) Protein Purification: Principles andPractice, New York: Springer-Verlag.

ADP-ribosyltransferase Activity

ADP-ribosylation results in the transfer of one adenosine diphosphateribose group from a donor (e.g., NAD) to an amino acid residue (e.g.,cysteine, threonine) of a substrate (e.g., glutamate dehydrogenase,aldehyde dehydrogenase, or a histone). An ADP-ribosyltransferase is anenzyme (e.g. a protein or polypeptide) that can catalyze anADP-ribosylation reaction.

For example, it is possible to monitor the addition of ADP from a[³²P]-NAD to a substrate (e.g., glutamate dehydrogenase, aldehydedehydrogenase, or histones). In one embodiment, theADP-ribosyltransferase activity is evaluated by providing a protein tobe evaluated (about 0-1 μg) (e.g., a Sirt4 protein) to a reaction buffercomprising, e.g., 50 mM Tris-HCl, pH 8.0, 4 mM MgCl₂, 0.2 mM DTT, 1 μMcold or nonradiolabeled NAD, 0.08 μM [³²P]-NAD, and admixing or gentlyvortexing to dilute, resuspend, or mix the protein. Substrates (e.g.,glutamate dehydrogenase, aldehyde dehydrogenase, or histones, about 0-1μg) are then added, and the reaction mixture is incubated at ambienttemperature (18-25° C.) for 30-120 minutes. The presence or absence ofADP-ribosylation products (e.g., ADP-ribosylated proteins) is detected,e.g., using autoradiography. The amount of ADP-ribosylation, forexample, in the presence and absence of an agent to be tested, can bedetermined using suitable techniques, including, but not limited to,densitometric scanning of autoradiographs or phosphoimaging techniquesof gels. (See Ausubel et al., Current Protocols in Molecular Biology,John Wiley & Sons (1999).)

Confirmation of ADP-ribosylation of substrates and, thus,ADP-ribosyltransferase activity of an agent can be performed, forexample, by adding a suitable amount of snake venom phosphodiesterase(e.g., 2 mg/ml, specific activity 1.5 U/mg) to the resulting product ofthe reaction mixture described above. The reaction product andphosphodiesterase are incubated at about 37° C. for about an hour.Absence of an autoradiographic band following phosphodiesterasedigestion, as compared with presence of an autoradiographic band in theabsence of digestion, indicates that the substrate was ADP-ribosylated.ADP-ribosyltransferase activity can also be verifies by the addition ofone or more specific ADP-ribosylation inhibitors, including, but notlimited to, novobiocin and coumermycin Al, to in vitro assays describedabove. The inhibitor(s) can be added before or after the addition of thesubstrate. The absence of a band in an autoradiograph following theaddition of a specific ADP-ribosylation inhibitor indicates that theagent has ADP-ribosyltransferase activity.

Exemplary substrates include, e.g., glutamate dehydrogenase (GDH),aldehyde dehydrogenase (ADH), adenine nucleotide transporter (ANT) andits homologs, e.g., mitochondrial carrier proteins, or histones, or afragment of any of the above. Substrates can be obtained from anyspecies of organism, including human, murine, or other mammal, otheranimals (e.g., nematode, fruit fly), or other organism, e.g., yeast. Inone embodiment, the substrate is obtained from the same species as theSIRT4 protein.

The fragment can be conserved, e.g., at or near the ADP ribosylationsite. Exemplary fragments of human GDH include: a fragment from a regionof about 1-50, 50-100, 100-150, 150-200, 250-300, 300-350, 350-400,400-450, 450-500, or 500-550.

Interaction Assays

In some embodiments, interaction with (e.g., binding to) Sirt4 can beassayed, e.g., in vitro or in a cell. The reaction mixture can include,e.g., a co-factor such as NAD and/or a NAD analog, a substrate or otherbinding partner or potentially interacting fragment thereof. Exemplarybinding partners include GDH, IDE, ANT, or interacting fragmentsthereof. Preferably the binding partner is a direct binding partner.

In other embodiments, the reaction mixture can include a Sirt4 bindingpartner, and compounds can be screened, e.g., in an in vitro assay, toevaluate the ability of a test compound to modulate interaction betweena Sirt4 and a Sirt4 binding partner. This type of assay can beaccomplished, for example, by coupling one of the components with aradioisotope or enzymatic label such that binding of the labeledcomponent to the other can be determined by detecting the labeledcompound in a complex. A component can be labeled with ¹²⁵I, ³⁵S, ³³P,³²P, ¹⁴C, or ³H, either directly or indirectly, and the radioisotopedetected by direct counting of radioemmission or by scintillationcounting. Alternatively, a component can be enzymatically labeled with,for example, horseradish peroxidase, alkaline phosphatase, orluciferase, and the enzymatic label detected by determination ofconversion of an appropriate substrate to product. Competition assayscan also be used to evaluate a physical interaction between a testcompound and a target.

Cell-free assays involve preparing a reaction mixture of the targetprotein (e.g., Sirt4) and the test compound under conditions and for atime sufficient to allow the two components to interact and bind, thusforming a complex that can be removed and/or detected.

The interaction between two molecules can also be detected, e.g., usinga fluorescence assay in which at least one molecule is fluorescentlylabeled. One example of such an assay includes fluorescence energytransfer (FET or FRET for fluorescence resonance energy transfer) (see,for example, U.S. Pat. No. 5,631,169; U.S. Pat. No. 4,868,103). Afluorophore label on the first, ‘donor’ molecule is selected such thatits emitted fluorescent energy will be absorbed by a fluorescent labelon a second, ‘acceptor’ molecule, which in turn is able to fluoresce dueto the absorbed energy. Alternately, the ‘donor’ protein molecule maysimply utilize the natural fluorescent energy of tryptophan residues.Labels are chosen that emit different wavelengths of light, such thatthe ‘acceptor’ molecule label may be differentiated from that of the‘donor’. Since the efficiency of energy transfer between the labels isrelated to the distance separating the molecules, the spatialrelationship between the molecules can be assessed. In a situation inwhich binding occurs between the molecules, the fluorescent emission ofthe ‘acceptor’ molecule label in the assay should be maximal. A FETbinding event can be conveniently measured through standard fluorometricdetection means well known in the art (e.g., using a fluorimeter).

Another example of a fluorescence assay is fluorescence polarization(FP). For FP, only one component needs to be labeled. A bindinginteraction is detected by a change in molecular size of the labeledcomponent. The size change alters the tumbling rate of the component insolution and is detected as a change in FP. See, e.g., Nasir et al.(1999) Comb Chem HTS 2:177-190; Jameson et al. (1995) Methods Enzymol246:283; Seethala et al. (1998) Anal Biochem. 255:257. Fluorescencepolarization can be monitored in multiwell plates, e.g., using thePOLARION™ reader (Tecan, Maennedorf, Switzerland). See, e.g., Parker etal. (2000) J Biomolecular Screening 5:77-88; and Shoeman, et al. (1999)Biochem 38:16802-16809.

In another embodiment, evaluating binding of a Sirt4 protein to acompound can include a real-time monitoring of the binding interaction,e.g., using Biomolecular Interaction Analysis (BIA) (see, e.g.,Sjolander and Urbaniczky (1991) Anal. Chem. 63:2338-2345 and Szabo etal. (1995) Curr. Opin. Struct. Biol. 5:699-705). “Surface plasmonresonance” or “BIA” detects biospecific interactions in real time,without labeling any of the interactants (e.g., BIAcore). Changes in themass at the binding surface (indicative of a binding event) result inalterations of the refractive index of light near the surface (theoptical phenomenon of surface plasmon resonance (SPR)), resulting in adetectable signal which can be used as an indication of real-timereactions between biological molecules.

In one embodiment, Sirt4 protein is anchored onto a solid phase. TheSirt4/test compound complexes anchored on the solid phase can bedetected at the end of the reaction, e.g., the binding reaction. Forexample, Sirt4 protein can be anchored onto a solid surface, and thetest compound, (which is not anchored), can be labeled, either directlyor indirectly, with detectable labels discussed herein.

It may be desirable to immobilize either Sirt4 protein or a Sirt4binding partner to facilitate separation of complexed from uncomplexedforms of one or both of the proteins, as well as to accommodateautomation of the assay. Binding of a test compound to Sirt4, orinteraction of Sirt4 with a second component in the presence and absenceof a candidate compound, can be accomplished in any vessel suitable forcontaining the reactants. Examples of such vessels include microtiterplates, test tubes, and micro-centrifuge tubes. In one embodiment, afusion protein can be provided which adds a domain that allows one orboth of the proteins to be bound to a matrix. For example,glutathione-S-transferase/mammalian homolog of a SIR2 fusion proteins orglutathione-S-transferase/target fusion proteins can be adsorbed ontoglutathione SEPHAROSE® beads (Sigma Chemical, St. Louis, Mo.) orglutathione derivatized microtiter plates, which are then combined withthe test compound or the test compound and either the non-adsorbedtarget protein or Sirt4, and the mixture incubated under conditionsconducive to complex formation (e.g., at physiological conditions forsalt and pH). Following incubation, the beads or microtiter plate wellsare washed to remove any unbound components, the matrix immobilized inthe case of beads, complex determined either directly or indirectly, forexample, as described above. Alternatively, the complexes can bedissociated from the matrix, and the level of Sirt4 binding or activitydetermined using standard techniques.

Other techniques for immobilizing either Sirt4 or a target molecule onmatrices include using conjugation of biotin and streptavidin.Biotinylated Sirt4 or target molecules can be prepared from biotin-NHS(N-hydroxy-succinimide) using techniques known in the art (e.g.,biotinylation kit, Pierce Chemicals, Rockford, Ill.), and immobilized inthe wells of streptavidin-coated 96 well plates (Pierce Chemical).

In order to conduct the assay, the non-immobilized component is added tothe coated surface containing the anchored component. After the reactionis complete, unreacted components are removed (e.g., by washing) underconditions such that any complexes formed will remain immobilized on thesolid surface. The detection of complexes anchored on the solid surfacecan be accomplished in a number of ways. Where the previouslynon-immobilized component is pre-labeled, the detection of labelimmobilized on the surface indicates that complexes were formed. Wherethe previously non-immobilized component is not pre-labeled, an indirectlabel can be used to detect complexes anchored on the surface, e.g.,using a labeled antibody specific for the immobilized component (theantibody, in turn, can be directly labeled or indirectly labeled with,e.g., a labeled anti-Ig antibody).

In one embodiment, this assay is performed utilizing antibodies reactivewith Sirt4 or target molecules, but which do not interfere with bindingof Sirt4 to its target molecule. Such antibodies can be derivatized tothe wells of the plate, and unbound target or Sirt4 trapped in the wellsby antibody conjugation. Methods for detecting such complexes, inaddition to those described above for the GST-immobilized complexes,include immunodetection of complexes using antibodies reactive withSirt4 or the target molecule, as well as enzyme-linked assays which relyon detecting an enzymatic activity associated with Sirt4 or the targetmolecule.

Alternatively, cell free assays can be conducted in a liquid phase. Insuch an assay, the reaction products are separated from unreactedcomponents, by any of a number of standard techniques, including but notlimited to: differential centrifugation (see, for example, Rivas, G.,and Minton, A. P., (1993) Trends Biochem Sci 18:284-7); chromatography(gel filtration chromatography, ion-exchange chromatography);electrophoresis (see, e.g., Ausubel, F. et al., eds. Current Protocolsin Molecular Biology 1999, J. Wiley: New York.); and immunoprecipitation(see, for example, Ausubel, F. et al., eds. (1999) Current Protocols inMolecular Biology, J. Wiley: New York). Such resins and chromatographictechniques are known to one skilled in the art (see, e.g., Heegaard, N.H., (1998) J Mol Recognit 11:141-8; Hage, D. S., and Tweed, S. A. (1997)J Chromatogr B Biomed Sci Appl. 699:499-525). Further, fluorescenceenergy transfer may also be conveniently utilized, as described herein,to detect binding without further purification of the complex fromsolution.

In a preferred embodiment, the assay includes contacting Sirt4 or abiologically active portion thereof with a known compound which bindsSirt4 to form an assay mixture, contacting the assay mixture with a testcompound, and determining the ability of the test compound to interactwith Sirt4, wherein determining the ability of the test compound tointeract with Sirt4 includes determining the ability of the testcompound to preferentially bind to Sirt4 or a biologically activeportion thereof, or to modulate the activity of a target molecule, ascompared to the known compound.

Sirt4 can, in vivo, interact with one or more cellular macromolecules,such as proteins. Such cellular macromolecules are referred to herein as“Sirt4 binding partners.” Exemplary Sirt4 binding partners include GDH,ANT, and IDE. Compounds that disrupt such interactions can be useful inregulating the activity of Sirt4. Such compounds can include, but arenot limited to molecules such as antibodies, peptides, and smallmolecules. Compounds that disrupt binding can themselves interact withSirt4 protein or with a Sirt4 binding partner.

To identify compounds that modulate (e.g., interfere with) theinteraction between the target product and its binding partner(s), forexample, a reaction mixture containing the target product and thebinding partner is prepared, under conditions and for a time sufficient,to allow the two products to form complex. In order to test aninhibitory agent, the reaction mixture is provided in the presence andabsence of the test compound. The test compound can be initiallyincluded in the reaction mixture, or can be added at a time subsequentto the addition of the target and its cellular or extracellular bindingpartner. Control reaction mixtures are incubated without the testcompound or with a placebo. The formation of any complexes between thetarget product and the cellular or extracellular binding partner is thendetected. The formation of a complex in the control reaction, but not inthe reaction mixture containing the test compound, indicates that thecompound interferes with the interaction of the target product and theinteractive binding partner. Additionally, complex formation withinreaction mixtures containing the test compound and normal target productcan also be compared to complex formation within reaction mixturescontaining the test compound and mutant target product. This comparisoncan be important in those cases wherein it is desirable to identifycompounds that disrupt interactions of mutant but not normal targetproducts.

These assays can be conducted in a heterogeneous or homogeneous format.Heterogeneous assays involve anchoring either the target product or thebinding partner onto a solid phase, and detecting complexes anchored onthe solid phase at the end of the reaction. In homogeneous assays, theentire reaction is carried out in a liquid phase. In either approach,the order of addition of reactants can be varied to obtain differentinformation about the compounds being tested. For example, testcompounds that interfere with the interaction between the targetproducts and the binding partners, e.g., by competition, can beidentified by conducting the reaction in the presence of the testsubstance. Alternatively, test compounds that disrupt preformedcomplexes, e.g., compounds with higher binding constants that displaceone of the components from the complex, can be tested by adding the testcompound to the reaction mixture after complexes have been formed. Thevarious formats are briefly described below.

In a heterogeneous assay system, either the target product or thepartner, is anchored onto a solid surface (e.g., a microtiter plate),while the non-anchored species is labeled, either directly orindirectly. The anchored species can be immobilized by non-covalent orcovalent attachments. Alternatively, an immobilized antibody specificfor the species to be anchored can be used to anchor the species to thesolid surface.

In order to conduct the assay, the partner of the immobilized species isexposed to the coated surface with or without the test compound. Afterthe reaction is complete, unreacted components are removed (e.g., bywashing) and any complexes formed will remain immobilized on the solidsurface. Where the non-immobilized species is pre-labeled, the detectionof label immobilized on the surface indicates that complexes wereformed. Where the non-immobilized species is not pre-labeled, anindirect label can be used to detect complexes anchored on the surface;e.g., using a labeled antibody specific for the initiallynon-immobilized species (the antibody, in turn, can be directly labeledor indirectly labeled with, e.g., a labeled anti-Ig antibody). Dependingupon the order of addition of reaction components, test compounds thatinhibit complex formation or that disrupt preformed complexes can bedetected.

Alternatively, the reaction can be conducted in a liquid phase in thepresence or absence of the test compound, the reaction productsseparated from unreacted components, and complexes detected; e.g., usingan immobilized antibody specific for one of the binding components toanchor any complexes formed in solution, and a labeled antibody specificfor the other partner to detect anchored complexes. Again, dependingupon the order of addition of reactants to the liquid phase, testcompounds that inhibit complex or that disrupt preformed complexes canbe identified.

In an alternate embodiment, a homogeneous assay can be used. Forexample, a preformed complex of the target product and the interactivecellular or extracellular binding partner product is prepared in thateither the target products or their binding partners are labeled, butthe signal generated by the label is quenched due to complex formation(see, e.g., U.S. Pat. No. 4,109,496 that utilizes this approach forimmunoassays). The addition of a test substance that competes with anddisplaces one of the species from the preformed complex will result inthe generation of a signal above background. In this way, testsubstances that disrupt target product-binding partner interaction canbe identified.

In yet another aspect, Sirt4 can be used as “bait proteins” in atwo-hybrid assay or three-hybrid assay (see, e.g., U.S. Pat. No.5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J.Biol. Chem. 268:12046-12054; Bartel et al. (1993) Biotechniques14:920-924; Iwabuchi et al. (1993) Oncogene 8:1693-1696; and BrentWO94/10300), to identify other Sirt4 binding proteins that may beinvolved in Sirt4 activity. In one embodiment, the two-hybrid assay isused to monitor an interaction between two components, e.g., Sirt4 and,e.g., GDH, ANT, IDE, or fragments thereof. The two hybrid assay can alsobe conducted in the presence of a test compound, and the assay is usedto determine whether the test compound enhances or diminishes theinteraction between the components.

Cell-Based Assays

Cell-based assays can be used to evaluate compounds for their ability tointeract with Sirt4 protein, e.g., bind or modulate the enzymaticactivity of a Sirt4 protein. Useful assays include assays in which aSirt4-associated parameter is evaluated. Other parameters that can beevaluated include parameters that assess insulin production orsecretion.

In addition, it is possible to evaluate the modification state of asubstrate in a Sirt4-expressing cell. For example, one can evaluate theADP-ribosylation state of a substrate, such as glutamate dehydrogenase(GDH), aldehyde dehydrogenase (ADH), or histones, or a fragment of anyof the above, or a Sirt4 binding partner. Optionally, the substrate canbe immunoprecipitated from an extract made from the Sirt4 expressingcell (e.g., contacted or not contacted with a test compound). Theprecipitated substrate can then be evaluated. In another variation, themodified form of the substrate is detected using a reagent thatdiscriminates between the modified and unmodified form. For example, thereagent is an antibody that specifically recognizes the ADP-ribosylatedform.

Another exemplary cell based assay can include contacting a cellexpressing a Sirt4 protein with a test compound and determining theability of the test compound to modulate (e.g. stimulate or inhibit) anactivity of a Sirt4 protein, and/or determine the ability of the testcompound to modulate expression of Sirt4, e.g., by detecting Sirt4nucleic acids (e.g., mRNA or cDNA) or proteins in the cell. Determiningthe ability of the test compound to modulate Sirt4 activity can beaccomplished, for example, by determining the ability of a Sirt4 proteinor nucleic acid to bind to or interact with a substrate (e.g., asdescribed above), to bind or interact with the test molecule, and bydetermining the ability of the test molecule to modulate a parameter,e.g., insulin secretion, insulin levels, or β-amyloid peptideaccumulation.

Cell-based systems can be used to identify compounds that decreaseexpression and/or activity and/or effect of Sirt4. Such cells can berecombinant or non-recombinant, such as cell lines that express SIRT4gene. In some embodiments, the cells can be recombinant ornon-recombinant cells which express a Sirt4 binding partner. Exemplarysystems include mammalian or yeast cells that express Sirt4, e.g., froma recombinant nucleic acid. In utilizing such systems, cells are exposedto compounds suspected of increasing expression and/or activity ofSirt4. After exposure, the cells are assayed, for example, for Sirt4expression or activity.

Alternatively, the cells may also be assayed for the activation orinhibition of the ADP-ribosylation function of Sirt4, or modulation ofinsulin secretion or β-amyloid peptide accumulation. In one embodiment,the levels of ADP-ribosylation of a mitochondrial protein, e.g.,glutamate dehydrogenase, are evaluated, e.g., in isolated mitochondria.In another embodiment, secreted insulin or β-amyloid peptide can bemeasured directly, e.g., with an immunoglobulin, e.g., by ELISA. Thecells can also be assayed for ATP levels or ATP/ADP ratio. ATP and ADPin sample extracts can be measured using chromatographic methods, asdescribed herein. ATP levels can also be measured by using cellstransfected with a reporter gene, such as a luciferase expressionconstruct designed to emit a luminescence signal that is directlycorrelated to ATP concentration (Kohler et al. (1998) FEBS Lett 441:97-102 and Kennedy et al. (1999) J Biol Chem 274:13281-91). ATP and ADPcan also be measured, e.g., using enzymatic methods, e.g., using theENLITEN® ATP Assay System (Promega, Madison, Wis.) or see Adra et al.(1987) Gene 60:65-74, U.S. Pat. No. 4,923,796.

A cell-based assay can be performed using a single cell, or a collectionof at least two or more cells. The cell can be a yeast cell (e.g.,Saccharomyces cerevisiae) or a mammalian cell, including but not limitedto somatic or embryonic cells (e.g., pancreatic or brain cells), HepG2cells, MIN6 cells, INS-1 cells, Chinese hamster ovary cells, HeLa cells,human 293 cells, and monkey COS-7 cells. The collection of cells canform a tissue. A “tissue” refers to a collection of similar cell types(such as epithelium, connective, muscle, and nerve tissue).

In another embodiment, modulators of Sirt4 gene expression areidentified. For example, a cell or cell free mixture is contacted with acandidate compound and the expression of Sirt4 mRNA or protein evaluatedrelative to the level of expression of Sirt4 mRNA or protein in theabsence of the candidate compound. When expression of the Sirt4 mRNA orprotein is greater in the presence of the candidate compound than in itsabsence, the candidate compound is identified as a stimulator of Sirt4mRNA or protein expression. Alternatively, when expression of Sirt4 mRNAor protein is less (statistically significantly less) in the presence ofthe candidate compound than in its absence, the candidate compound isidentified as an inhibitor of the Sirt4 mRNA or protein expression. Thelevel of Sirt4 mRNA or protein expression can be determined by methodsfor detecting Sirt4 mRNA or protein, e.g., using probes or antibodies,e.g., labeled probes or antibodies.

In addition to cell-based and in vitro assay systems, non-humanorganisms, e.g., transgenic non-human organisms or a model organism, canalso be used. A transgenic organism is one in which a heterologous DNAsequence is chromosomally integrated into the germ cells of the animal.A transgenic organism will also have the transgene integrated into thechromosomes of its somatic cells. Organisms of any species, including,but not limited to: yeast, worms, flies, fish, reptiles, birds, mammals(e.g., mice, rats, rabbits, guinea pigs, pigs, micro-pigs, and goats),and non-human primates (e.g., baboons, monkeys, chimpanzees) may be usedin the methods described herein.

A transgenic cell or animal used in the methods disclosed herein caninclude a transgene that encodes, e.g., Sirt4. The transgene can encodea protein that is normally exogenous to the transgenic cell or animal,including a human protein, e.g., human Sirt4. The transgene can belinked to a heterologous or a native promoter. A transgenic animal canalso be produced with reduced expression or activity of, e.g., Sirt4,e.g., a Sirt4 deletion or mutant. Methods of making transgenic cells andanimals are known in the art.

Accordingly, in another embodiment, this disclosure features a method ofidentifying a compound as a candidate of treatment of a metabolicdisorder, e.g., a disorder characterized by an insufficiency or excessof insulin, e.g., type 1 diabetes, type 2 diabetes, or hyperinsulinemia.The method includes: providing a compound which interacts with, e.g.,binds to, Sirt4; evaluating the effect of the compound on insulinsecretion; and further evaluating the effect of the test compound on asubject, e.g., an animal model, e.g., an animal model for a metabolicdisorder, e.g., type 1 diabetes or type 2 diabetes. Exemplary animalmodels are described below. The interaction between a test compound andSirt4 can be evaluated by any of the methods described herein, e.g.,using cell-based assays or cell-free in vitro assays.

Accordingly, in another embodiment, this disclosure features a method ofidentifying a compound as a candidate of treatment of a β-amyloiddisorder, e.g., a disorder characterized by β-amyloid accumulation,e.g., Alzheimer's disease. The method includes: providing a compoundwhich interacts with, e.g., binds to, Sirt4; evaluating the effect ofthe compound on β-amyloid accumulation; and further evaluating theeffect of the test compound on a subject, e.g., an animal model, e.g.,an animal model for a β-amyloid disorder, e.g., Alzheimer's disease.Exemplary animal models are described below. The interaction between atest compound and Sirt4 can be evaluated by any of the methods describedherein, e.g., using cell-based assays or cell-free in vitro assays.

Test Compounds

A “compound” or “test compound” can be any chemical compound, forexample, a macromolecule (e.g., a polypeptide, a protein complex, or anucleic acid) or a small molecule (e.g., an amino acid, a nucleotide, anorganic or inorganic compound). The test compound can have a formulaweight of less than about 10 000 grams per mole, less than 5 000 gramsper mole, less than 1 000 grams per mole, or less than about 500 gramsper mole. The test compound can be naturally occurring (e.g., a herb ora nature product), synthetic, or both. Examples of macromolecules areproteins, protein complexes, and glycoproteins, nucleic acids, e.g.,DNA, RNA (e.g., double stranded RNA or RNAi) and PNA (peptide nucleicacid). Examples of small molecules are peptides, peptidomimetics (e.g.,peptoids), amino acids, amino acid analogs, polynucleotides,polynucleotide analogs, nucleotides, nucleotide analogs, nucleosides,glycosidic compounds, organic or inorganic compounds e.g., heteroorganicor organometallic compounds. One exemplary type of protein compound isan antibody or a modified scaffold domain protein. A test compound canbe the only substance assayed by the method described herein.Alternatively, a collection of test compounds can be assayed eitherconsecutively or concurrently by the methods described herein.

In one preferred embodiment, high throughput screening methods involveproviding a combinatorial chemical or peptide library containing a largenumber of potential therapeutic compounds (potential modulator or ligandcompounds). Such “combinatorial chemical libraries” or “ligandlibraries” are then screened in one or more assays, as described herein,to identify those library members (particular chemical species orsubclasses) that display a desired characteristic activity. Thecompounds thus identified can serve as conventional “lead compounds” orcan themselves be used as potential or actual therapeutics.

A combinatorial chemical library is a collection of diverse chemicalcompounds generated by either chemical synthesis or biologicalsynthesis, by combining a number of chemical “building blocks” such asreagents. For example, a linear combinatorial chemical library such as apolypeptide library is formed by combining a set of chemical buildingblocks (amino acids) in every possible way for a given compound length(i.e., the number of amino acids in a polypeptide compound). Millions ofchemical compounds can be synthesized through such combinatorial mixingof chemical building blocks.

Preparation and screening of combinatorial chemical libraries is wellknown to those of skill in the art. Such combinatorial chemicallibraries include, but are not limited to, peptide libraries (see, e.g.,U.S. Pat. 5,010,175; Furka, Int. J. Pept. Prot. Res. 37:487-493 (1991)and Houghton et al., Nature 354:84-88 (1991)). Other chemistries forgenerating chemical diversity libraries can also be used. Suchchemistries include, but are not limited to: peptoids (e.g., PCTPublication No. WO 91/19735), encoded peptides (e.g., PCT PublicationNo. WO 93/20242), random bio-oligomers (e.g., PCT Publication No. WO92/00091), benzodiazepines (e.g., U.S. Pat. No. 5,288,514), diversomerssuch as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc.Nat. Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides(Hagihara et al., J Amer. Chem. Soc. 114:6568 (1992)), nonpeptidalpeptidomimetics with glucose scaffolding (Hirschmann et al., J Amer.Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses of smallcompound libraries (Chen et al., J. Amer. Chem. Soc. 116:2661 (1994)),oligocarbamates (Cho et al., Science 261:1303 (1993)), and/or peptidylphosphonates (Campbell et al., J Org. Chem. 59:658 (1994)), nucleic acidlibraries (see Ausubel, Berger and Sambrook, all supra), peptide nucleicacid libraries (see, e.g., U.S. Pat. 5,539,083), antibody libraries(see, e.g., Vaughn et al., Nature Biotechnology, 14(3):309-314 (1996)and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et al.,Science, 274:1520-1522 (1996) and U.S. Pat. No. 5,593,853), smallorganic molecule libraries (see, e.g., benzodiazepines, Baum C&EN, Jan18, page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588;thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974;pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholinocompounds, U.S. Pat. No. 5,506,337; benzodiazepines, U.S. Pat. No.5,288,514, and the like). Additional examples of methods for thesynthesis of molecular libraries can be found in the art, for examplein: DeWitt et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90:6909; Erb etal. (1994) Proc. Natl. Acad. Sci. USA 91:11422; Zuckermann et al.(1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261:1303;Carrell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al.(1994) Angew. Chem. Int. Ed. Engl. 33:2061; and Gallop et al. (1994) JMed. Chem. 37:1233.

Some exemplary libraries are used to generate variants from a particularlead compound. One method includes generating a combinatorial library inwhich one or more functional groups of the lead compound are varied,e.g., by derivatization. Thus, the combinatorial library can include aclass of compounds which have a common structural feature (e.g.,framework).

Devices for the preparation of combinatorial libraries are commerciallyavailable (see, e.g., 357 MPS, 390 MPS, Advanced Chem Tech, LouisvilleKy.; SYMPHONY™, Rainin, Woburn, Mass.; 433A Applied Biosystems, FosterCity, Calif.; 9050 Plus, Millipore, Bedford, Mass.). In addition,numerous combinatorial libraries are themselves commercially available(see, e.g., ComGenex, Princeton, N.J.; Asinex, Moscow, RU, Tripos, Inc.,St. Louis, Mo.; ChemStar, Ltd, Moscow, RU; 3D Pharmaceuticals, Exton,Pa.; Martek Biosciences, Columbia, Md.; etc.).

Test compounds can also be obtained from: biological libraries; peptoidlibraries (libraries of molecules having the functionalities ofpeptides, but with a novel, non-peptide backbone which are resistant toenzymatic degradation but which nevertheless remain bioactive; see,e.g., Zuckermann, R. N. et al. (1994) J Med. Chem. 37:2678-85);spatially addressable parallel solid phase or solution phase libraries;synthetic library methods requiring deconvolution; the “one-beadone-compound” library method; and synthetic library methods usingaffinity chromatography selection. The biological libraries includelibraries of nucleic acids and libraries of proteins. Some nucleic acidlibraries encode a diverse set of proteins (e.g., natural and artificialproteins; others provide, for example, functional RNA and DNA moleculessuch as nucleic acid aptamers or ribozymes. A peptoid library can bemade to include structures similar to a peptide library. (See also Lam(1997) Anticancer Drug Des. 12:145). A library of proteins may beproduced by an expression library or a display library (e.g., a phagedisplay library).

Libraries of compounds may be presented in solution (e.g., Houghten(1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (Ladner,U.S. Pat. No. 5,223,409), spores (Ladner U.S. Pat. No. 5,223,409),plasmids (Cull et al. (1992) Proc Natl Acad Sci USA 89:1865-1869) or onphage (Scott and Smith (1990) Science 249:386-390; Devlin (1990) Science249:404-406; Cwirla et al. (1990) Proc. Natl. Acad. Sci. 87:6378-6382;Felici (1991) J. Mol. Biol. 222:301-310).

Antibodies

Immunoglobulins can be produced that bind to Sirt4 or a Sirt4 bindingpartner (e.g., a protein that interacts with Sirt4). For example, animmunoglobulin can bind to Sirt4 and prevent Sirt4 enzymatic activity oran interaction between Sirt4 and a Sirt4 binding partner (e.g., GDH,IDE, or ANT). In one embodiment, the immunoglobulin is human, humanized,deimmunized, or otherwise non-antigenic in the subject.

In one embodiment, an immunoglobulin can be produced that candistinguish between mature, processed Sirt4 and unprocessed Sirt4, e.g.,an antibody that binds preferentially to one form relative to the other.For example, an antibody that binds preferentially to the matureprocessed form can be an antibody that binds to amino acid residues29-32 of a Sirt4 whose N-terminus begins at a residue corresponding toresidue 29 of SEQ ID NO:1. An antibody that binds preferentially to anunprocessed Sirt4 can be an antibody that binds to amino acid residues1-28 of SEQ ID NO:1.

Antibodies that bind specifically to mono-ADP-ribose can be utilized todistinguish ADP-ribosylated substrates form non-ADP-ribosylatedsubstrates (see, e.g., Meyer and Hilz (1986) Eur JBiochem 155:157-65).

An immunoglobulin can be, for example, an antibody or an antigen-bindingfragment thereof. As used herein, the term “immunoglobulin” refers to aprotein consisting of one or more polypeptides that include one or moreimmunoglobulin variable domain sequences. A typical immunoglobulinincludes at least a heavy chain immunoglobulin variable domain and alight chain immunoglobulin variable domain. An immunoglobulin proteincan be encoded by immunoglobulin genes. The recognized humanimmunoglobulin genes include the kappa, lambda, alpha (IgA1 and IgA2),gamma (IgG1, IgG2, IgG3, IgG4), delta, epsilon and mu constant regiongenes, as well as the myriad immunoglobulin variable region genes.Full-length immunoglobulin “light chains” (about 25 kDa or 214 aminoacids) are encoded by a variable region gene at the NH2-terminus (about110 amino acids) and a kappa or lambda constant region gene at theCOOH-terminus. Full-length immunoglobulin “heavy chains” (about 50 kDaor 446 amino acids), are similarly encoded by a variable region gene(about 116 amino acids) and one of the other aforementioned constantregion genes, e.g., gamma (encoding about 330 amino acids). The term“antigen-binding fragment” of an antibody (or simply “antibody portion”or “fragment”), as used herein, refers to one or more fragments of afull-length antibody that retain the ability to specifically bind to theantigen. Examples of antigen-binding fragments include: (i) a Fabfragment, a monovalent fragment consisting of the VL, VH, CL and CHIdomains; (ii) a F(ab′)2 fragment, a bivalent fragment comprising two Fabfragments linked by a disulfide bridge at the hinge region; (iii) a Fdfragment consisting of the VH and CH1 domains; (iv) a Fv fragmentconsisting of the VL and VH domains of a single arm of an antibody, (v)a dAb fragment (Ward et al., (1989) Nature 341:544-546), which consistsof a VH domain; and (vi) an isolated complementarity determining region(CDR). Furthermore, although the two domains of the Fv fragment, VL andVH, are coded for by separate genes, they can be joined, usingrecombinant methods, by a synthetic linker that enables them to be madeas a single protein chain in which the VL and VH regions pair to formmonovalent molecules (known as single chain Fv (scFv); see e.g., Bird etal. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl.Acad. Sci. USA 85:5879-5883). Such single chain antibodies are alsoencompassed within the term “antigen-binding fragment” of an antibody.These antibody fragments are obtained using conventional techniques, andthe fragments are screened for utility in the same manner as are intactantibodies.

In one embodiment, the antibody against Sirt4 or another protein is afully human antibody (e.g., an antibody made in a mouse which has beengenetically engineered to produce an antibody from a humanimmunoglobulin sequence), or a non-human antibody, e.g., a rodent (mouseor rat), goat, primate (e.g., monkey). Preferably, the non-humanantibody is a rodent (mouse or rat antibody). Method of producing rodentantibodies are known in the art. Non-human antibodies can be modified,e.g., humanized or deimmunized. Human monoclonal antibodies can begenerated using transgenic mice carrying the human immunoglobulin genesrather than the mouse system (see, e.g., WO 91/00906 and WO 92/03918).Other methods for generating immunoglobulin ligands include phagedisplay (e.g., as described in U.S. Pat. No. 5,223,409 and WO 92/20791).

Sirt4 Modulating Nucleic Acids

Nucleic acid molecules (e.g., DNA or RNA molecules) can be used tomodulate (e.g., increase or decrease) Sirt4 expression or activity.

A Sirt4 modulator can be a nucleic acid molecule designed to increaseexpression or activity of Sirt4, e.g., an exogenous copy of the Sirt4gene under the control of a promoter, e.g., a targeted promoter.

A Sirt4 modulator can be a siRNA, anti-sense RNA, or a ribozyme, whichcan decrease the expression of Sirt4. In some aspects, a cell or subjectcan be treated with a compound that modulates the expression of a gene,e.g., a nucleic acid which modulates, e.g., decreases, expression of apolypeptide which inhibits Sirt4. Such approaches includeoligonucleotide-based therapies such as RNA interference, antisense,ribozymes, and triple helices.

Gene expression can be modified by gene silencing using double-strandRNA (Sharp (1999) Genes and Development 13: 139-141). RNAi methods,including double-stranded RNA interference (dsRNAi) or small interferingRNA (siRNA), have been extensively documented in a number of organisms,including mammalian cells and the nematode C. elegans (Fire, A., et al,Nature, 391, 806-811, 1998).

dsRNA can be delivered to cells or to an organism to antagonize Sirt4 oranother protein described herein. For example, a dsRNA that iscomplementary to a Sirt4 nucleic acid can silence protein expression ofthe Sirt4. The dsRNA can include a region that is complementary to acoding region of a Sirt4 nucleic acid, e.g., a 5′ coding region, aregion encoding a Sirt4 core domain, a 3′ coding region, or a non-codingregion, e.g., a 5′ or 3′ untranslated region. dsRNA can be produced,e.g., by transcribing a cassette (in vitro or in vivo) in bothdirections, for example, by including a T7 promoter on either side ofthe cassette. The insert in the cassette is selected so that it includesa sequence complementary to the Sirt4 nucleic acid. The sequence neednot be full length, for example, an exon, or between 19-50 nucleotidesor 50-200 nucleotides. The sequence can be from the 5′ half of thetranscript, e.g., within 1000, 600, 400, or 300 nucleotides of the ATG.See also, the HISCRIBE™ RNAi Transcription Kit (New England Biolabs,Ma.) and Fire, A. (1999) Trends Genet. 15, 358-363. dsRNA can bedigested into smaller fragments. See, e.g., US Patent Application2002-0086356 and 2003-0084471.

In one embodiment, an siRNA is used. siRNAs are small double strandedRNAs (dsRNAs) that optionally include overhangs. For example, the duplexregion is about 18 to 25 nucleotides in length, e.g., about 19, 20, 21,22, 23, or 24 nucleotides in length. Typically, the siRNA sequences areexactly complementary to the target mRNA. It may also be possible toagonize activity of a Sirt4 by using an siRNA to inhibit a negativeregulator of the Sirt4.

Double-stranded inhibitory RNA can also be used to selectively reducethe expression of one allele of a gene and not the other, therebyachieving an approximate 50% reduction in the expression of a Sirt4antagonist polypeptide. See Garrus et al. (2001) Cell 107(1):55-65.

“Ribozymes” are enzymatic RNA molecules which cleave at specific sitesin RNA. Ribozymes that can specifically cleave nucleic acids that encodeor that are required for the expression of Sirt4 may be designedaccording to well-known methods.

A nucleic acid for modulating Sirt4 expression, activity, or functioncan be inserted into a variety of DNA constructs and vectors for thepurposes of gene therapy. Vectors include plasmids, cosmids, artificialchromosomes, viral elements, and RNA vectors (e.g., based on RNA virusgenomes). The vector can be competent to replicate in a host cell or tointegrate into a host DNA. Viral vectors include, e.g., replicationdefective retroviruses, adenoviruses and adeno-associated viruses.

Examples of vectors include replication defective retroviral vectors,adenoviral vectors and adeno-associated viral vectors. Adenoviralvectors suitable for use by the methods disclosed herein include(Ad.RSV.lacZ), which includes the Rous sarcoma virus promoter and thelacZ reporter gene as well as (Ad.CMV.lacZ), which includes thecytomegalovirus promoter and the lacZ reporter gene. Methods for thepreparation and use of viral vectors are described in WO 96/13597, WO96/33281, WO 97/15679, and Trapnell et al., Curr. Opin. Biotechnol.5(6):617-625, 1994, the contents of which are incorporated herein byreference.

A gene therapy vector is a vector designed for administration to asubject, e.g., a mammal, such that a cell of the subject is able toexpress a therapeutic gene contained in the vector. The therapeutic genemay encode a protein (e.g., Sirt4). The therapeutic gene can also beused to provide a non-coding transcript, e.g., an antisense RNA, aribozyme, or a dsRNA, that targets an RNA of a sirtuin gene, e.g., aSirt4 gene).

The gene therapy vector can contain regulatory elements, e.g., a 5′regulatory element, an enhancer, a promoter, a 5′ untranslated region, asignal sequence, a 3′ untranslated region, a polyadenylation site, and a3′ regulatory region. For example, the 5′ regulatory element, enhanceror promoter can regulate transcription of the DNA encoding thetherapeutic polypeptide or other transcript. The regulation can betissue specific. For example, the regulation can restrict transcriptionof the desired gene, e.g., Sirt4, to pancreas cells, e.g., pancreaticislet β-cells. For example, the regulation can restrict transcription ofthe desired gene, e.g., Sirt4, to nervous tissue cells, e.g., neuronalor microglial cells. Alternatively, regulatory elements can be includedthat respond to an exogenous drug, e.g., a steroid, tetracycline, or thelike. Thus, the level and timing of expression of the therapeuticnucleic acid can be controlled.

Gene therapy vectors can be prepared for delivery as naked nucleic acid,as a component of a virus, or of an inactivated virus, or as thecontents of a liposome or other delivery vehicle. See, e.g., US2003-0143266 and 2002-0150626. In one embodiment, the nucleic acid isformulated in a lipid-protein-sugar matrix to form microparticles.,e.g., having a diameter between 50 nm to 10 micrometers. The particlesmay be prepared using any known lipid (e.g.,dipalmitoylphosphatidylcholine, DPPC), protein (e.g., albumin), or sugar(e.g., lactose).

The gene therapy vectors can be delivered using a viral system.Exemplary viral vectors include vectors from retroviruses, e.g., Moloneyretrovirus, adenoviruses, adeno-associated viruses, and lentiviruses,e.g., Herpes simplex viruses (HSV). HSV, for example, is potentiallyuseful for infecting nervous system cells. See, e.g., US 2003/0147854,2002/0090716, 2003/0039636, 2002/0068362, and 2003/0104626. The genedelivery agent, e.g., a viral vector, can be produced from recombinantcells which produce the gene delivery system.

A gene therapy vector can be administered to a subject, for example, byintravenous injection, by local administration (see U.S. Pat. No.5,328,470) or by stereotactic injection (see e.g., Chen et al. (1994)Proc. Natl. Acad. Sci. USA 91:3054-3057). The gene therapy agent can befurther formulated, for example, to delay or prolong the release of theagent by means of a slow release matrix. One method of providing atherapeutic agent, is by inserting a gene therapy vector into cellsharvested from a subject. The cells are infected, for example, with aretroviral gene therapy vector, and grown in culture. The subject isthen replenished with the infected culture cells. The subject ismonitored for recovery and for production of the therapeutic polypeptideor nucleic acid.

The disclosure also includes vectors, such as gene therapy vectors, thatinclude a Sirt4 regulatory sequence (e.g., a Sirt4 promoter) forregulating a coding sequence other than Sirt4.

Cell-based therapeutic methods include introducing a nucleic acid thatprovides a therapeutic activity operably linked to a promoter into acell in culture. The therapeutic nucleic acid can provide the desiredmodulation of Sirt4 activity in a cultured cell, e.g., an increase ordecrease in Sirt4 activity to an insulin-secreting cell. Further, it isalso possible to modify cells, e.g., stem cells, using nucleic acidrecombination, e.g., to insert a transgene, e.g., a transgene thatprovides a therapeutic activity. The modified stem cell can beadministered to a subject. Methods for cultivating stem cells in vitroare described, e.g., in US Application 2002/0081724. In some examples,the stem cells can be induced to differentiate in the subject andexpress the transgene. For example, the stem cells can be differentiatedinto pancreas, liver, adipose, neuronal or skeletal muscle cells. Thestem cells can be derived from a lineage that produces cells of thedesired tissue type, e.g., pancreas, liver, adipose, neuronal, orskeletal muscle cells.

Modifications to nucleic acid molecules may be introduced as a means ofincreasing intracellular stability and half-life. Exemplarymodifications include the addition of flanking sequences ofribonucleotides or deoxyribonucleotides to the 5′ and/or 3′ ends of themolecule or the use of phosphorothioate or 2′ O-methyl rather thanphosphodiesterase linkages within the oligodeoxyribonucleotide backbone.

Artificial Transcription Factors

Artificial transcription factors can also be used to regulate genesdescribed herein, e.g., genes encoding Sirt4, GDH, IDE, or ANT.

The artificial transcription factor can be designed or selected from alibrary. The protein can include one or more zinc finger domains. Forexample, the protein can be prepared by selection in vitro (e.g., usingphage display, U.S. Pat. No. 6,534,261) or in vivo, or by design basedon a recognition code (see, e.g., WO 00/42219 and U.S. Pat. No.6,511,808). See, e.g., Rebar et al. (1996) Methods Enzymol 267:129;Greisman and Pabo (1997) Science 275:657; Isalan et al. (2001) Nat.Biotechnol 19:656; and Wu et al. (1995) Proc. Nat. Acad. Sci. USA 92:344for, among other things, methods for creating libraries of varied zincfinger domains.

Optionally, the artificial transcription factor can be fused to atranscriptional regulatory domain, e.g., an activation domain toactivate transcription or a repression domain to repress transcription.The artificial transcription factor can itself be encoded by aheterologous nucleic acid that is delivered to a cell (e.g., a vectordescribed herein) or the transcription factor itself can be delivered toa cell (see, e.g., U.S. Pat. No. 6,534,261). The heterologous nucleicacid that includes a sequence encoding the transcription factor can beoperably linked to an inducible promoter, e.g., to enable fine controlof the level of the transcription factor in the cell.

Gene Expression and Transcript Analysis

Different aspects disclosed herein can include evaluating expression ofone or more genes described herein (e.g., genes encoding Sirt4, insulin,GDH, IDE, and ANT). Expression of a gene can be evaluated by detectingan mRNA, e.g., the transcript from the gene of interest or detecting aprotein, e.g., the protein encoded by the gene of interest. Geneexpression can also be measured, e.g., using an indirect method, e.g.,using a reporter construct (e.g., as described below).

Reporter genes for measuring expression of Sirt4, or a Sirt4 target orbinding partner, can be made by operably linking a regulatory sequence,e.g., a regulatory sequence of the Sirt4 gene, to a sequence encoding areporter gene. A number of methods are available for designing reportergenes. For example, the sequence encoding the reporter protein can belinked in frame to all or part of the sequence that is normallyregulated by the regulatory sequence. Such constructs can be referred toas translational fusions. It is also possible to link the sequenceencoding the reporter protein to only regulatory sequences, e.g., the 5′untranslated region, TATA box, and/or sequences upstream of the mRNAstart site. Such constructs can be referred to as transcriptionalfusions. Still other reporter genes can be constructed by inserting oneor more copies (e.g., a multimer of three, four, or six copies) of aregulatory sequence into a neutral or characterized promoter.

Reporter constructs can be used to evaluate expression of any gene,e.g., genes encoding Sirt4, insulin, GDH, ANT, or IDE, or other genedescribed herein.

Exemplary reporter proteins include chloramphenicol acetyltransferase,green fluorescent protein and other fluorescent proteins (e.g.,artificial variants of GFP), beta-lactamase, beta-galactosidase,luciferase, and so forth. The reporter protein can be any protein otherthan the protein encoded by the endogenous gene that is subject toanalysis. Epitope tags, e.g., flag or his tags, can also be used.

Exemplary methods for evaluating mRNAs include northern analysis,RT-PCR, microarray hybridization, SAGE, differential display, andmonitoring reporter genes. Exemplary methods for evaluating proteinsinclude immunoassays (e.g., ELISAs, immunoprecipitations, westerns),2D-gel electrophoresis, and mass spectroscopy. It is possible toevaluate fewer than 100, e.g., less than 20, 10, 5, 4, or 3 differentmolecular species, e.g., to only evaluate the expression of the gene ofinterest, although it is typically useful to include at least one or twocontrols (e.g., a house keeping gene). It is also possible to evaluatemultiple molecular species, e.g., in parallel, e.g., at least 10, 50,20, 100, or more different species. See, e.g., the usage of microarrays,e.g. as described below.

One method for comparing transcripts uses nucleic acid microarrays thatinclude a plurality of addresses, each address having a probe specificfor a particular transcript, at least one of which is specific for agene of interest, e.g., a gene encoding Sirt4, insulin, GDH, IDE, andANT. Such arrays can include at least 100, or 1000, or 5000 differentprobes, so that a substantial fraction, e.g., at least 10, 25, 50, or75% of the genes in an organism are evaluated. mRNA can be isolated froma cell or other sample of the organism. The mRNA can be reversedtranscribed into labeled cDNA. The labeled cDNAs are hybridized to thenucleic acid microarrays. The arrays are detected to quantitate theamount of cDNA that hybridizes to each probe, thus providing informationabout the level of each transcript.

Methods for making and using nucleic acid microarrays are well known.For example, nucleic acid arrays can be fabricated by a variety ofmethods, e.g., photolithographic methods (see, e.g., U.S. Pat. Nos.5,143,854; 5,510,270; and. 5,527,681), mechanical methods (e.g.,directed-flow methods as described in U.S. Pat. No. 5,384,261), pinbased methods (e.g., as described in U.S. Pat. No. 5,288,514), and beadbased techniques (e.g., as described in PCT US/93/04145). The probe canbe a single-stranded nucleic acid, a double-stranded nucleic acid (e.g.,which is denatured prior to or during hybridization), or a nucleic acidhaving a single-stranded region and a double-stranded region.Preferably, the probe is single-stranded. The probe can be selected by avariety of criteria, and preferably is designed by a computer programwith optimization parameters. The probe can be selected to hybridize toa sequence rich (e.g., non-homopolymeric) region of the nucleic acid.The T_(m) of the probe can be optimized by prudent selection of thecomplementarity region and length. Ideally, the T_(m) of all probes onthe array is similar, e.g., within 20, 10, 5, 3, or 2° C. of oneanother. A database scan of available sequence information for a speciescan be used to determine potential cross-hybridization and specificityproblems.

The isolated mRNA from samples for comparison can be reversedtranscribed and optionally amplified, e.g., by rtPCR, e.g., as describedin (U.S. Pat. No. 4,683,202). The nucleic acid can be labeled duringamplification, e.g., by the incorporation of a labeled nucleotide.Examples of preferred labels include fluorescent labels, e.g.,red-fluorescent dye Cy5 (Amersham) or green-fluorescent dye Cy3(Amersham), and chemiluminescent labels, e.g., as described in U.S. Pat.No. 4,277,437. Alternatively, the nucleic acid can be labeled withbiotin, and detected after hybridization with labeled streptavidin,e.g., streptavidin-phycoerythrin (Molecular Probes).

The labeled nucleic acid can be contacted to the array. In addition, acontrol nucleic acid or a reference nucleic acid can be contacted to thesame array. The control nucleic acid or reference nucleic acid can belabeled with a label other than the sample nucleic acid, e.g., one witha different emission maximum. Labeled nucleic acids can be contacted toan array under hybridization conditions. The array can be washed, andthen imaged to detect fluorescence at each address of the array.

A general scheme for producing and evaluating profiles can include thefollowing. The extent of hybridization at an address is represented by anumerical value and stored, e.g., in a vector, a one-dimensional matrix,or one-dimensional array. The vector x has a value for each address ofthe array. For example, a numerical value for the extent ofhybridization at a first address is stored in variable x_(a). Thenumerical value can be adjusted, e.g., for local background levels,sample amount, and other variations. Nucleic acid is also prepared froma reference sample and hybridized to an array (e.g., the same or adifferent array), e.g., with multiple addresses. The vector y isconstruct identically to vector x. The sample expression profile and thereference profile can be compared, e.g., using a mathematical equationthat is a function of the two vectors. The comparison can be evaluatedas a scalar value, e.g., a score representing similarity of the twoprofiles. Either or both vectors can be transformed by a matrix in orderto add weighting values to different nucleic acids detected by thearray.

The expression data can be stored in a database, e.g., a relationaldatabase such as a SQL database (e.g., Oracle or Sybase databaseenvironments). The database can have multiple tables. For example, rawexpression data can be stored in one table, wherein each columncorresponds to a nucleic acid being assayed (e.g., one or more of genesencoding Sirt4, insulin, GDH, ANT, or IDE, or other gene describedherein), and each row corresponds to a sample. A separate table canstore identifiers and sample information, e.g., the batch number of thearray used, date, and other quality control information.

Other methods for quantitating mRNAs include: quantitative RT-PCR. Inaddition, two nucleic acid populations can be compared at the molecularlevel, e.g., using subtractive hybridization or differential display toevaluate differences in mRNA expression, e.g., between a cell ofinterest and a reference cell.

Pharmaceutical Compositions

An agent that modulates activity of Sirt4 can be incorporated into apharmaceutical composition, e.g., a composition that includes apharmaceutically acceptable carrier.

As used herein the language “pharmaceutically acceptable carrier”includes solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents, and thelike, compatible with pharmaceutical administration. Supplementaryactive compounds can also be incorporated into the compositions.

A pharmaceutical composition is formulated to be compatible with itsintended route of administration. Examples of routes of administrationinclude parenteral, e.g., intravenous, intradermal, subcutaneous, oral(e.g., inhalation), transdermal (topical), transmucosal, and rectaladministration. Solutions or suspensions used for parenteral,intradermal, or subcutaneous application can include the followingcomponents: a sterile diluent such as water for injection, salinesolution, fixed oils, polyethylene glycols, glycerine, propylene glycolor other synthetic solvents; antibacterial agents such as benzyl alcoholor methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediaminetetraacetic acid;buffers such as acetates, citrates or phosphates and agents for theadjustment of tonicity such as sodium chloride or dextrose. pH can beadjusted with acids or bases, such as hydrochloric acid or sodiumhydroxide. The parenteral preparation can be enclosed in ampoules,disposable syringes or multiple dose vials made of glass or plastic.

Toxicity and therapeutic efficacy of such compounds can be determined bystandard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., for determining the LD₅₀ (the dose lethal to 50% of thepopulation) and the ED₅₀ (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects isthe therapeutic index and it can be expressed as the ratio LD₅₀/ED₅₀.Compounds which exhibit high therapeutic indices are preferred. Whilecompounds that exhibit toxic side effects may be used, care should betaken to design a delivery system that targets such compounds to thesite of affected tissue in order to minimize potential damage touninfected cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofsuch compounds lies preferably within a range of circulatingconcentrations that include the ED₅₀ with little or no toxicity. Thedosage may vary within this range depending upon the dosage formemployed and the route of administration utilized. For any compound usedin the methods disclosed herein, the therapeutically effective dose canbe estimated initially from cell culture assays. A dose may beformulated in animal models to achieve a circulating plasmaconcentration range that includes the IC₅₀ (i.e., the concentration ofthe test compound which achieves a half-maximal inhibition of symptoms)as determined in cell culture. Such information can be used to moreaccurately determine useful doses in humans. Levels in plasma may bemeasured, for example, by high performance liquid chromatography.

Examples of modulators of Sirt4 activity include nucleic acids thatencode a Sirt4, or fragments thereof, nucleic acids that inhibit Sirt4gene expression, and polypeptides that have a Sirt4 activity, fragmentsthereof, as well as antibodies that bind to and/or inhibit a Sirt4. Suchmodulators can be provided as a pharmaceutical composition. Other typesof modulators include small molecule inhibitors and activators, e.g., asdescribed herein.

A therapeutically effective amount of protein or polypeptide (i.e., aneffective dosage) includes ranges, e.g., from about 0.001 to 30 mg/kgbody weight, preferably about 0.01 to 25 mg/kg body weight. The skilledartisan will appreciate that certain factors may influence the dosageand timing required to effectively treat a subject, including but notlimited to the severity of the disease or disorder, previous treatments,the general health and/or age of the subject, and other diseasespresent. Moreover, treatment of a subject with a therapeuticallyeffective amount of a protein, polypeptide, or antibody can include asingle treatment or, preferably, can include a series of treatments.

A pharmaceutical composition is formulated to be compatible with itsintended route of administration. Examples of routes of administrationinclude parenteral, e.g., intravenous, intradermal, subcutaneous, oral(e.g., inhalation), transdermal (topical), transmucosal, and rectaladministration. Solutions or suspensions used for parenteral,intradermal, or subcutaneous application can include the followingcomponents: a sterile diluent such as water for injection, salinesolution, fixed oils, polyethylene glycols, glycerine, propylene glycolor other synthetic solvents; antibacterial agents such as benzyl alcoholor methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediaminetetraacetic acid;buffers such as acetates, citrates or phosphates and agents for theadjustment of tonicity such as sodium chloride or dextrose. pH can beadjusted with acids or bases, such as hydrochloric acid or sodiumhydroxide. The parenteral preparation can be enclosed in ampoules,disposable syringes or multiple dose vials made of glass or plastic.

In one embodiment, a composition that includes a modulator of Sirt4activity is used to modulate (e.g., increase, decrease) the amount ofinsulin secreted by the pancreas.

In one embodiment, a composition that includes a modulator of Sirt4activity is used to decrease the accumulation of β-amyloid peptide.

Diabetes

An agent that modulates Sirt4 expression or activity can be used totreat or prevent diabetes. The agent can be administered to a subject inan amount effective to treat, prevent, or ameliorate at least onesymptom of diabetes. For example, an agent that decreases Sirt4expression or activity can be used to increase insulin secretion, e.g.,in a hypoinsulinemic subject. An agent that, e.g., increases Sirt4expression can be used to decrease insulin secretion, e.g., in ahyperinsulinemic subject.

Examples of diabetes include insulin dependent diabetes mellitus andnon-insulin dependent diabetes. For example the method includesadministering to a patient having diabetes or at risk of diabetes acompound described herein.

For example, a compound described herein can be administered to asubject in a therapeutically effective amount to increase insulinsecretion in response to glucose, decrease insulin secretion in responseto glucose, decrease gluconeogenesis, improve glycemic control (i.e.,lower fasting blood glucose), or normalize insulin sensitivity. Thecompound can be administered to a subject suffering from or at risk fordiabetes or obesity.

In some instances, a patient can be identified as being at risk ofdeveloping diabetes (pre-diabetes) by having impaired glucose tolerance(IGT), insulin resistance, obesity, metabolic syndrome X, misfunction ofglucose regulation by liver, fat, brain, and/or muscle, or fastinghyperglycemia.

Insulin dependent diabetes mellitus (Type 1 diabetes) is an autoimmunedisease, where insulitis leads to the destruction of pancreatic β-cells.At the time of clinical onset of type 1 diabetes mellitus, significantnumber of insulin producing β cells are destroyed and only 15% to 40%are still capable of insulin production (McCulloch et al. (1991)Diabetes 40:673-679). β-cell failure results in a life long dependenceon daily insulin injections and exposure to the acute and latecomplication of the disease.

Type 2 diabetes mellitus is a metabolic disease of impaired glucosehomeostasis characterized by hyperglycemia, or high blood sugar, as aresult of defective insulin action which manifests as insulinresistance, defective insulin secretion, or both. A patient with Type 2diabetes mellitus has abnormal carbohydrate, lipid, and proteinmetabolism associated with insulin resistance and/or impaired insulinsecretion. The disease leads to pancreatic beta cell destruction andeventually absolute insulin deficiency. Without insulin, high glucoselevels remain in the blood. The long term effects of high blood glucoseinclude blindness, renal failure, and poor blood circulation to theseareas, which can lead to foot and ankle amputations. Early detection iscritical in preventing patients from reaching this severity. Themajority of patients with diabetes have the non-insulin dependent formof diabetes, currently referred to as Type 2 diabetes mellitus.

This disclosure also includes methods of treating disorders related toor resulting from diabetes, for example end organ damage, diabeticgastroparesis, diabetic neuropathy, cardiac dysrythmia, etc.

Exemplary molecular models of Type II diabetes include: a transgenicmouse having defective Nkx-2.2 or Nkx-6.1; (U.S. Pat. No. 6,127,598);Zucker Diabetic Fatty fa/fa (ZDF) rat. (U.S. Pat. No. 6,569,832); andRhesus monkeys, which spontaneously develop obesity and subsequentlyfrequently progress to overt type 2 diabetes (Hotta et al., Diabetes,50:1126-33 (2001); and a transgenic mouse with a dominant-negative IGF-1receptor (KR-IGF-1R) having Type 2 diabetes-like insulin resistance.

Metabolic Syndrome

An agent that modulates Sirt4 expression or activity can be used totreat or prevent metabolic syndrome. The agent can be administered to asubject in an amount effective to treat,.prevent, or ameliorate at leastone symptom of metabolic syndrome.

Metabolic syndrome (e.g., Syndrome X) is a syndrome characterized by agroup of metabolic risk factors in one person. These factors include twoor more of (particularly three, four, five or more, or all of): centralobesity (excessive fat tissue in and around the abdomen), atherogenicdyslipidemia (blood fat disorders—mainly high triglycerides and low HDLcholesterol—that foster plaque buildups in artery walls); insulinresistance or glucose intolerance (the body can't properly use insulinor blood sugar); prothrombotic state (e.g., high fibrinogen orplasminogen activator inhibitor-1 (PAI-1) in the blood); raised bloodpressure (i.e., hypertension) (130/85 mmHg or higher); andproinflammatory state (e.g., elevated high-sensitivity C-reactiveprotein in the blood).

The underlying causes of this syndrome include overweight/obesity,physical inactivity and genetic factors. People with metabolic syndromeare at increased risk of coronary heart disease, other diseases relatedto plaque buildups in artery walls (e.g., stroke and peripheral vasculardisease), and type 2 diabetes. Metabolic syndrome is closely associatedwith a generalized metabolic disorder called insulin resistance, inwhich the body fails to utilize insulin efficiently.

Alzheimer's Disease

An agent that modulates Sirt4 expression or activity, preferably onethat increases Sirt4 expression or activity, can be used to treat orprevent Alzheimer's Disease (AD). The agent can be an agent describedherein or an agent identified by a method described herein. The agentcan be administered in an amount effective to treat, prevent, orameliorate at least one symptom of AD.

Alzheimer's Disease (AD) is a complex neurodegenerative disease thatresults in the irreversible loss of neurons and is an example of aneurodegenerative disease that has symptoms caused at least in part byprotein aggregation.

Clinical hallmarks of Alzheimer's disease include progressive impairmentin memory, judgment, orientation to physical surroundings, and language.Neuropathological hallmarks of AD include region-specific neuronal loss,amyloid plaques, and neurofibrillary tangles.

Amyloid plaques are extracellular plaques containing the β amyloidpeptide (also known as Aβ, or Aβ42), which is a cleavage product of theβ-amyloid precursor protein (also known as APP). Neurofibrillary tanglesare insoluble intracellular aggregates composed of filaments of theabnormally hyperphosphorylated microtubule-associated protein, tau.Amyloid plaques and neurofibrillary tangles may contribute to secondaryevents that lead to neuronal loss by apoptosis (Clark and Karlawish,Ann. Intern. Med. 138(5):400-410 (2003)). For example, β-amyloid inducescaspase-2-dependent apoptosis in cultured neurons (Troy et al. J.Neurosci. 20(4):1386-1392). The deposition of plaques in vivo maytrigger apoptosis of proximal neurons in a similar manner.

Mutations in genes encoding APP, presenilin-1, and presenilin-2 havebeen implicated in early-onset AD (Lendon et al. JAMA 227:825 (1997)).Mutations in these proteins have been shown to enhance proteolyticprocessing of APP via an intracellular pathway that produces Aβ.Aberrant regulation of Aβ processing may be central to the formation ofamyloid plaques and the consequent neuronal damage associated withplaques.

A variety of criteria, including genetic, biochemical, physiological,and cognitive criteria, can be used to evaluate AD in a subject.Symptoms and diagnosis of AD are known to medical practitioners. Someexemplary symptoms and markers of AD are presented below. Informationabout these indications and other indications known to be associatedwith AD can be used as an “AD-related parameter.” An AD-relatedparameter can include qualitative or quantitative information. Anexample of quantitative information is a numerical value of one or moredimensions, e.g., a concentration of a protein or a tomographic map.Qualitative information can include an assessment, e.g., a physician'scomments or a binary (“yes/no”) and so forth. An AD-related parameterincludes information that indicates that the subject is not diagnosedwith AD or does not have a particular indication of AD, e.g., acognitive test result that is not typical of AD or a geneticapolipoprotein E (APOE) polymorphism not associated with AD.

Progressive cognitive impairment is a hallmark of AD. This impairmentcan present as decline in memory, judgment, decision making, orientationto physical surroundings, and language (Nussbaum and Ellis, New Eng. JMed. 348(14):1356-1364 (2003)). Exclusion of other forms of dementia canassist in making a diagnosis of AD.

Neuronal death leads to progressive cerebral atrophy in AD patients.Imaging techniques (e.g., magnetic resonance imaging, or computedtomography) can be used to detect AD-associated lesions in the brainand/or brain atrophy.

The insulin degrading enzyme (IDE) can degrade β-amyloid protein inneuronal and microglial cell cultures (Qiu et al. (1997) J. Biol. Chem.272:6641-6; Qiu et al. (1998) J. Biol. Chem. 273:32730-8; Vekrellis etal. (2000) J. Neurosci. 20:1657-65; Sudoh et al. (2002) Biochemistry41:1091-9), and can eliminate the neurotoxicity of β-amyloid protein(Mukherjee et al. (2000) J. Neurosci. 20:8745-9). Furthermore, IDE −/−mice presented chronic elevation of β-amyloid protein, similar to thatseen in AD patients (Farris et al. (2003) Proc Nat'l Acad Sci USA100:4162-7).

AD patients may exhibit biochemical abnormalities that result from thepathology of the disease. For example, levels of tau protein in thecerebrospinal fluid is elevated in AD patients (Andreasen, N. et al.Arch Neurol. 58:349-350 (2001)). Levels of amyloid beta 42 (Aβ42)peptide can be reduced in CSF of AD patients (Galasko, D., et al. Arch.Neurol. 55:937-945 (1998)). Levels of Aβ42 can be increased in theplasma of AD patients (Ertekein-Taner, N., et al. Science 290:2303-2304(2000)). Techniques to detect biochemical abnormalities in a sample froma subject include cellular, immunological, and other biological methodsknown in the art. For general guidance, see, e.g., techniques describedin Sambrook & Russell, Molecular Cloning: A Laboratory Manual, 3rdEdition, Cold Spring Harbor Laboratory, N.Y. (2001), Ausubel et al.,Current Protocols in Molecular Biology (Greene Publishing Associates andWiley Interscience, N.Y. (1989), (Harlow, E. and Lane, D. (1988)Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y.), and updated editions thereof.

For example, antibodies, other immunoglobulins, and other specificbinding ligands can be used to detect a biomolecule, e.g., a protein orother antigen associated with AD. For example, one or more specificantibodies can be used to probe a sample. Various formats are possible,e.g., ELISAs, fluorescence-based assays, western blots, and proteinarrays. Methods of producing polypeptide arrays are described in theart, e.g., in De Wildt et al. (2000). Nature Biotech. 18,989-994;Lueking et al. (1999). Anal. Biochem. 270, 103-111; Ge, H. (2000).Nucleic Acids Res. 28, e3, I-VII; MacBeath, G., and Schreiber, S. L.(2000). Science 289, 1760-1763; and WO 99/51773A1. Proteins can also beanalyzed using mass spectroscopy, chromatography, electrophoresis,enzyme interaction or using probes that detect post-translationalmodification (e.g., a phosphorylation, ubiquitination, glycosylation,methylation, or acetylation).

Metabolites that are associated with AD can be detected by a variety ofmeans, including enzyme-coupled assays, using labeled precursors, andnuclear magnetic resonance (NMR). For example, NMR can be used todetermine the relative concentrations of phosphate-based compounds in asample, e.g., creatine levels. Other metabolic parameters such as redoxstate, ion concentration (e.g., Ca²⁺) (e.g., using ion-sensitive dyes),and membrane potential can also be detected (e.g., using patch-clamptechnology).

In one embodiment, a non-human animal model of AD (e.g., a mouse model)is used, e.g., to evaluate a compound or a therapeutic regimen, e.g., ofan agent described herein. For example, U.S. Pat. No. 6,509,515describes one such model animal which is naturally able to be used withlearning and memory tests. The animal expresses an amyloid precursorprotein (APP) sequence at a level in brain tissues such that the animaldevelops a progressive neurologic disorder within a short period of timefrom birth, generally within a year from birth, preferably within 2 to 6months, from birth. The APP protein sequence is introduced into theanimal, or an ancestor of the animal, at an embryonic stage, preferablythe one cell, or fertilized oocyte, stage, and generally not later thanabout the 8-cell stage. The zygote or embryo is then developed to termin a pseudo-pregnant foster female. The amyloid precursor protein genesare introduced into an animal embryo so as to be chromosomallyincorporated in a state which results in super-endogenous expression ofthe amyloid precursor protein and the development of a progressiveneurologic disease in the cortico-limbic areas of the brain, areas ofthe brain which are prominently affected in progressive neurologicdisease states such as AD. The gliosis and clinical manifestations inaffected transgenic animals model neurologic disease. The progressiveaspects of the neurologic disease are characterized by diminishedexploratory and/or locomotor behavior and diminished 2-deoxyglucoseuptake/utilization and hypertrophic gliosis in the cortico-limbicregions of the brain. Other animal models are also described in U.S.Pat. Nos. 5,387,742; 5,877,399; 6,358,752; and 6,187,992.

Additionally, glutamate is a key neurotransmitter. Sirt4 can function toregulate glutamate dehydrogenase, and thus glutamate levels in thebrain. Sirt4 can play an important role in monitoring synapse and neuronfunction. Mice with an activating mutation in glutamate dehydrogenasesuffer from neurological problems,

Parkinson's Disease

Parkinson's disease includes neurodegeneration of dopaminergic neuronsin the substantia nigra resulting in the degeneration of thenigrostriatal dopamine system that regulates motor function. Thispathology, in turn, leads to motor dysfunctions. (see, e.g., andLotharius et al., Nat. Rev. Neurosci., 3:932-42 (2002).) Exemplary motorsymptoms include: akinesia, stooped posture, gait difficulty, posturalinstability, catalepsy, muscle rigidity, and tremor. Exemplary non-motorsymptoms include: depression, lack of motivation, passivity, dementiaand gastrointestinal dysfunction (see, e.g., Fahn, Ann. N.Y. Acad. Sci.,991:1-14 (2003) and Pfeiffer, Lancet Neurol., 2:107-16 (2003))Parkinson's has been observed in 0.5 to 1 percent of persons 65 to 69years of age and 1 to 3 percent among persons 80 years of age and older.(see, e.g., Nussbaum et al., N. Engl. J. Med., 348:1356-64 (2003)).

An agent that modulates Sirt4 activity can be used to ameliorate atleast one symptom of a subject that has Parkinson's disease.

Molecular markers of Parkinson's disease include reduction in aromaticL-amino acid decarboxylase (AADC). (see, e.g., US Appl 20020172664);loss of dopamine content in the nigrostriatal neurons (see, e.g., Fahn,Ann. N.Y. Acad. Sci., 991:1-14 (2003) and Lotharius et al., Nat. Rev.Neurosci., 3:932-42 (2002)). In some familial cases, PD is linked tomutations in single genes encoding alpha-synuclein and parkin (an E3ubiquitin ligase) proteins. (e.g., Riess et al., J. Neurol. 250 Suppl1:13-10 (2003) and Nussbaum et al., N. Engl. J. Med., 348:1356-64(2003)). A missense mutation in a neuron-specific C-terminal ubiquitinhydrolase gene is also associated with Parkinson's. (e.g., Nussbaum etal., N. Engl. J. Med., 348:1356-64 (2003))

A compound or library of compounds described herein can be evaluated ina non-human animal model of Parkinson's disease. Exemplary animal modelsof Parkinson's disease include primates rendered parkinsonian bytreatment with the dopaminergic neurotoxin 1-methyl-4 phenyl1,2,3,6-tetrahydropyridine (MPTP) (see, e.g., US Appl 20030055231 andWichmann et al., Ann. N.Y. Acad. Sci., 991:199-213 (2003);6-hydroxydopamine-lesioned rats (e.g., Lab. Anim. Sci.,49:363-71(1999)); and transgenic invertebrate models (e.g., Lakso et al., J.Neurochem., 86:165-72 (2003) and Link, Mech. Ageing Dev., 122:1639-49(2001)).

Evaluating Huntington's Disease

An agent that modulates the activity of Sirt4 can be used to ameliorateat least one symptom of Huntington's disease in a subject.

A variety of methods are available to evaluate and/or monitorHuntington's disease. A variety of clinical symptoms and indicia for thedisease are known. Huntington's disease causes a movement disorder,psychiatric difficulties and cognitive changes. The degree, age ofonset, and manifestation of these symptoms can vary. The movementdisorder can include quick, random, dance-like movements called chorea.

One method for evaluating Huntington's disease uses the UnifiedHuntington's disease Rating Scale (UNDRS). It is also possible to useindividual tests alone or in combination to evaluate if at least onesymptom of Huntington's disease is ameliorated. The UNDRS is describedin Movement Disorders (vol. 11:136-142,1996) and Marder et al. Neurology(54:452-458, 2000). The UNDRS quantifies the severity of Huntington'sDisease. It is divided into multiple subsections: motor, cognitive,behavioral, functional. In one embodiment, a single subsection is usedto evaluate a subject. These scores can be calculated by summing thevarious questions of each section. Some sections (such as chorea anddystonia) can include grading each extremity, face, bucco-oral-ligual,and trunk separately.

Exemplary motor evaluations include: ocular pursuit, saccade initiation,saccade velocity, dysarthria, tongue protrusion, finger tap ability,pronate/supinate, a fist-hand-palm sequence, rigidity of arms,bradykinesia, maximal dystonia (trunk, upper and lower extremities),maximal chorea (e.g., trunk, face, upper and lower extremities), gait,tandem walking, and retropulsion. An exemplary treatment can cause achange in the Total Motor Score 4(TMS-4), a subscale of the UHDRS, e.g.,over a one-year period.

A number of animal model system for Huntington's disease are available.See, e.g., Brouillet, Functional Neurology 15(4): 239-251 (2000); Ona etal. Nature 399: 263-267 (1999), Bates et al. Hum Mol Genet. 6(10):1633-7(1997); Hansson et al. J. of Neurochemistry 78: 694-703; andRubinsztein, D. C., Trends in Genetics, Vol. 18, No. 4, pp. 202-209 (areview on various animal and non-human models of HD).

Genetic Information

SIRT4 genetic information can be obtained, e.g., by evaluating geneticmaterial (e.g., DNA or RNA) from a subject (e.g., as described below).Genetic information refers to any indication about nucleic acid sequencecontent at one or more nucleotides. Genetic information can include, forexample, an indication about the presence or absence of a particularpolymorphism, e.g., one or more nucleotide variations. Exemplarypolymorphisms include a single nucleotide polymorphism (SNP), arestriction site or restriction fragment length, an insertion, aninversion, a deletion, a repeat (e.g., trinucleotide repeat, aretroviral repeat), and so forth.

Exemplary SIRT4 SNPs include: rs16950058; rs12425285; rs12424555;rs12307919; rs12300927; rs11834400; rs11614455; rs11613753; rs11609118;rs11412750; rs11378799; rs11065078; rs11065077; rs11065075; rs2905543;rs2701643; rs2522141; rs2522139; rs2522138; rs2522130; rs2522129;rs2464297; rs2464296; rs2428384; rs2261612; rs13461273; rs13461272;rs6400038; and rs6399397.

It is possible to digitally record or communicate genetic information ina variety of ways. Typical representations include one or more bits, ora text string. For example, a biallelic marker can be described usingtwo bits. In one embodiment, the first bit indicates whether the firstallele (e.g., the minor allele) is present, and the second bit indicateswhether the other allele (e.g., the major allele) is present. Formarkers that are multi-allelic, e.g., where greater than two alleles arepossible, additional bits can be used as well as other forms of encoding(e.g., binary, hexadecimal text, e.g., ASCII or Unicode, and so forth).In some embodiments, the genetic information describes a haplotype,e.g., a plurality of polymorphisms on the same chromosome. However, inmany embodiments, the genetic information is unphased.

Methods of Evaluating Genetic Material

There are numerous methods for evaluating genetic material to providegenetic information. These methods can be used to evaluate a SIRT4 locusas well as other loci.

Nucleic acid samples can analyzed using biophysical techniques (e.g.,hybridization, electrophoresis, and so forth), sequencing, enzyme-basedtechniques, and combinations-thereof. For example, hybridization ofsample nucleic acids to nucleic acid microarrays can be used to evaluatesequences in an mRNA population and to evaluate genetic polymorphisms.Other hybridization based techniques include sequence specific primerbinding (e.g., PCR or LCR); Southern analysis of DNA, e.g., genomic DNA;Northern analysis of RNA, e.g., mRNA; fluorescent probe based techniques(see, e.g., Beaudet et al. (2001) Genome Res. 11(4):600-8); and allelespecific amplification. Enzymatic techniques include restriction enzymedigestion; sequencing; and single base extension (SBE). These and othertechniques are well known to those skilled in the art.

Electrophoretic techniques include capillary electrophoresis andSingle-Strand Conformation Polymorphism (SSCP) detection (see, e.g.,Myers et al. (1985) Nature 313:495-8 and Ganguly (2002) Hum Mutat.19(4):334-42). Other biophysical methods include denaturing highpressure liquid chromatography (DHPLC).

In one embodiment, allele specific amplification technology that dependson selective PCR amplification may be used to obtain geneticinformation. Oligonucleotides used as primers for specific amplificationmay carry the mutation of interest in the center of the molecule (sothat amplification depends on differential hybridization) (Gibbs et al.(1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3′ end of oneprimer where, under appropriate conditions, mismatch can prevent, orreduce polymerase extension (Prossner (1993) Tibtech 11:238). Inaddition, it is possible to introduce a restriction site in the regionof the mutation to create cleavage-based detection (Gasparini et al.(1992) Mol. Cell Probes 6:1). In another embodiment, amplification canbe performed using Taq ligase for amplification (Barany (1991) Proc.Natl. Acad. Sci USA 88:189). In such cases, ligation will occur only ifthere is a perfect match at the 3′ end of the 5′ sequence making itpossible to detect the presence of a known mutation at a specific siteby looking for the presence or absence of amplification.

Enzymatic methods for detecting sequences include amplificationbased-methods such as the polymerase chain reaction (PCR; Saiki, et al.(1985) Science 230, 1350-1354) and ligase chain reaction (LCR; Wu. etal. (1989) Genomics 4, 560-569; Barringer et al. (1990), Gene 1989,117-122; F. Barany. 1991, Proc. Natl. Acad. Sci. USA 1988, 189-193);transcription-based methods utilize RNA synthesis by RNA polymerases toamplify nucleic acid (U.S. Pat. No. 6,066,457; U.S. Pat. No. 6,132,997;U.S. Pat. No. 5,716,785; Sarkar et al., Science (1989) 244:331-34;Stofler et al., Science (1988) 239:491); NASBA (U.S. Pat. Nos.5,130,238; 5,409,818; and 5,554,517); rolling circle amplification (RCA;U.S. Pat. Nos. 5,854,033 and 6,143,495) and strand displacementamplification (SDA; U.S. Pat. Nos. 5,455,166 and 5,624,825).Amplification methods can be used in combination with other techniques.

Other enzymatic techniques include sequencing using polymerases, e.g.,DNA polymerases and variations thereof such as single base extensiontechnology. See, e.g., U.S. Pat. No. 6,294,336; U.S. Pat. No. 6,013,431;and U.S. Pat. No. 5,952,174.

Mass spectroscopy (e.g., MALDI-TOF mass spectroscopy) can be used todetect nucleic acid polymorphisms. In one embodiment, (e.g., theMassEXTEND™ assay, SEQUENOM, Inc.), selected nucleotide mixtures,missing at least one dNTP and including a single ddNTP is used to extenda primer that hybridizes near a polymorphism. The nucleotide mixture isselected so that the extension products between the differentpolymorphisms at the site create the greatest difference in molecularsize. The extension reaction is placed on a plate for mass spectroscopyanalysis.

Fluorescence based detection can also be used to detect nucleic acidpolymorphisms. For example, different terminator ddNTPs can be labeledwith different fluorescent dyes. A primer can be annealed near orimmediately adjacent to a polymorphism, and the nucleotide at thepolymorphic site can be detected by the type (e.g., “color”) of thefluorescent dye that is incorporated.

Hybridization to microarrays can also be used to detect polymorphisms,including SNPs. For example, a set of different oligonucleotides, withthe polymorphic nucleotide at varying positions with theoligonucleotides can be positioned on a nucleic acid array. The extentof hybridization as a function of position and hybridization tooligonucleotides specific for the other allele can be used to determinewhether a particular polymorphism is present. See, e.g., U.S. Pat. No.6,066,454.

In one implementation, hybridization probes can include one or moreadditional mismatches to destabilize duplex formation and sensitize theassay. The mismatch may be directly adjacent to the query position, orwithin 10, 7, 5, 4, 3, or 2 nucleotides of the query position.Hybridization probes can also be selected to have a particular T_(m),e.g., between 45-60° C., 55-65° C., or 60-75° C. In a multiplex assay,T_(m)'s can be selected to be within 5, 3, or 2° C. of each other, e.g.,probes for rs1800591 and rs2866164 can be selected with these criteria.

It is also possible to directly sequence the nucleic acid for aparticular genetic locus, e.g., by amplification and sequencing, oramplification, cloning and sequence. High throughput automated (e.g.,capillary or microchip based) sequencing apparati can be used. In stillother embodiments, the sequence of a protein of interest is analyzed toinfer its genetic sequence. Methods of analyzing a protein sequenceinclude protein sequencing, mass spectroscopy, sequence/epitope specificimmunoglobulins, and protease digestion.

Any combination of the above methods can also be used. The above methodscan be used to evaluate any genetic locus, e.g., in a method foranalyzing genetic information from particular groups of individuals orin a method for analyzing a polymorphism associated with a metabolicdisorder, e.g., diabetes, or other disorder described herein, e.g., theSIRT4 locus.

Evaluating Markers of a Metabolic Disorder, e.g., Diabetes, or OtherDisorder Described Herein

A variety of criteria, including genetic, biochemical, physiological,and cognitive criteria, can be used to evaluate a metabolic disorder,e.g., diabetes, or other disorder described herein in a subject.Symptoms and diagnosis of a metabolic disorder, e.g., diabetes, or otherdisorder described herein are known to medical practitioners. Someexemplary symptoms and markers of a metabolic disorder, e.g., diabetes,or other disorder described herein are presented below. Informationabout these indications and other indications known to be associatedwith a metabolic disorder, e.g., diabetes, or other disorder describedherein can be used as a parameter associated with the disorder.

A parameter can include qualitative or quantitative information. Anexample of quantitative information is a numerical value of one or moredimensions, e.g., a concentration of a protein or a tomographic map.Qualitative information can include an assessment, e.g., a physician'scomments or a binary (“yes”/“no”) and so forth. An parameter can includeinformation that indicates that the subject is not diagnosed with ametabolic disorder, e.g., diabetes, or other disorder described hereinor does not have a particular indication of a metabolic disorder, e.g.,diabetes, or other disorder described herein.

Techniques to detect biochemical abnormalities in a sample from asubject include cellular, immunological, and other biological methodsknown in the art. For general guidance, see, e.g., techniques describedin Sambrook & Russell, Molecular Cloning: A Laboratory Manual, 3^(rd)Edition, Cold Spring Harbor Laboratory, N.Y. (2001), Ausubel et al.,Current Protocols in Molecular Biology (Greene Publishing Associates andWiley Interscience, N.Y. (1989), (Harlow, E. and Lane, D. (1988)Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y.), and updated editions thereof.

For example, antibodies, other immunoglobulins, and other specificbinding ligands can be used to detect a biomolecule, e.g., a protein orother antigen associated with a metabolic disorder, e.g., diabetes, orother disorder described herein. For example, one or more specificantibodies can be used to probe a sample. Various formats are possible,e.g., ELISAs, fluorescence-based assays, Western blots, and proteinarrays. Methods of producing polypeptide arrays are described in theart, e.g., in De Wildt et al. (2000). Nature Biotech. 18, 989-994;Lueking et al. (1999). Anal. Biochem. 270, 103-111; Ge, H. (2000).Nucleic Acids Res. 28, e3, I-VII; MacBeath, G., and Schreiber, S. L.(2000). Science 289, 1760-1763; and WO 99/51773A1.

Proteins can also be analyzed using mass spectroscopy, chromatography,electrophoresis, enzyme interaction or using probes that detectpost-translational modification (e.g., a phosphorylation,ubiquitination, glycosylation, methylation, or acetylation).

Nucleic acid expression can be detected in cells from a subject, e.g.,removed by surgery, extraction, post-mortem or other sampling (e.g.,blood, CSF). Expression of one or more genes can be evaluated, e.g., byhybridization based techniques, e.g., Northern analysis, RT-PCR, SAGE,and nucleic acid arrays. Nucleic acid arrays are useful for profilingmultiple mRNA species in a sample. A nucleic acid array can be generatedby various methods, e.g., by photolithographic methods (see, e.g., U.S.Pat. Nos. 5,143,854; 5,510,270; and 5,527,681), mechanical methods(e.g., directed-flow methods as described in U.S. Pat. No. 5,384,261),pin-based methods (e.g., as described in U.S. Pat. No. 5,288,514), andbead-based techniques (e.g., as described in PCT US/93/04145).

Metabolites that are associated with a metabolic disorder, e.g.,diabetes, or other disorder described herein can be detected by avariety of means, including enzyme-coupled assays, using labeledprecursors, and nuclear magnetic resonance (NMR). For example, NMR canbe used to determine the relative concentrations of phosphate-basedcompounds in a sample, e.g., creatine levels. Other metabolic parameterssuch as redox state, ion concentration (e.g., Ca²⁺)(e.g., usingion-sensitive dyes), and membrane potential can also be detected (e.g.,using patch-clamp technology).

Information about an a metabolic disorder, e.g., diabetes, or otherdisorder described herein-associated marker can be recorded and/orstored in a computer-readable format. Typically the information islinked to a reference about the subject and also is associated (directlyor indirectly) with information about the identity of one or morenucleotides in the subject's SIRT4 genes.

Identifying Relevant Genotypes

Methods for identifying genotypes associated with a metabolic disorder,e.g., diabetes, or other disorder described herein can includecomparisons to one or more reference sequences or an association studyamong individuals that have a particular characteristic, e.g., aparticular parameter, e.g., associated with a disorder described herein,or a diagnosis of a metabolic disorder, e.g., diabetes, or otherdisorder described herein diagnosis.

Multiple sets of reference sequences may be used for comparison.Exemplary reference sequences include sequences from subjects at riskfor or diagnosed with a metabolic disorder, e.g., diabetes, or otherdisorder described herein and sequences from subjects that are not atrisk for or diagnosed with a metabolic disorder, e.g., diabetes, orother disorder described herein.

By evaluating one or more genetic loci, it is possible to determine anassociation for each locus or for each allele of each locus, and aphenotype. One type of test of association is the G-Test, but otherstatistical measures can also be used. A high degree of association,e.g., a high ch-square statistic, can indicate that a particular locusis associated with a state (e.g., a phenotype). This type ofassociational study can be used to map a genetic locus that isassociated with the state. Associated loci can be used, e.g., fordiagnostic evaluations (e.g., genetic counseling, risk evaluation,prophylactic care, care management, and so forth) and for research(e.g., identifying targets for therapeutics).

As seen herein, it is also possible to identify genes associated withdisorders by using a method that includes: a) identifying a plurality ofhuman individuals characterized by a disorder or having a geneticrelationship with an subject characterized by the disorder; and b)comparing distribution of a plurality of genetic markers among thesubjects of the first plurality to distribution of markers of theplurality of genetic markers among subjects of a second plurality ofhuman subjects, wherein the human subjects of the second plurality haveattained at least 90, 95, 98, or 100 years of age. For example, theplurality of genetic markers includes at least one, 10, 20, 30 or 50markers from each chromosome. The method can further include evaluatinga measure of linkage disequilibrium (e.g., a LOD score). For example,each subject of the first plurality is suffering or at risk for anage-associated disorder or each subject of the first plurality isgenetically related to an subject suffering or at risk for anage-associated disorder.

In one embodiment, the first plurality includes at least 50, 100, 150,200, or 300 subjects. In one embodiment, the human subjects of thesecond plurality are free of an a metabolic disorder, e.g., diabetes, orother disorder described herein diagnosis. For example, the humansubjects of the second plurality are cognitively intact at the age of85, 90, 95, 98, or 100 and/or the human subjects of the second pluralityare free of a symptom or diagnosis of the disorder. In one embodiment,the second plurality includes at least 50, 100, 150, 200, 300, 500 or800 subjects.

Pharmacogenomics

Both prophylactic and therapeutic methods of treatment may bespecifically tailored or modified, based on knowledge obtained from apharmacogenomics analysis. In particular, a subject can be treated basedon the presence or absence of a genetic polymorphism associated with ametabolic disorder, e.g., diabetes, or other disorder described herein,e.g., a polymorphism associated with the SIRT4 locus.

Pharmacogenomics allows a clinician or physician to target prophylacticor therapeutic treatments to patients who will most benefit from thetreatment and to avoid the treatment of patients who will experiencetoxic or other undesirable drug-related side effects. In particular, adiet or drug that affects a metabolic disorder, e.g., diabetes, or otherdisorder described herein can be prescribed as a function of thesubject's SIRT4 locus. For example, if the individual's SIRT4 locusincludes an allele that is predisposed to a metabolic disorder, e.g.,diabetes, or other disorder described herein relative to other alleles,the individual can be indicated for a prophylactic treatment for a drugthat alleviates a metabolic disorder, e.g., diabetes, or other disorderdescribed herein. In another example, the individual is placed in amonitoring program, e.g., to closely monitor for physical manifestationsof a metabolic disorder, e.g., diabetes, or other disorder describedherein onset.

These and other aspects of the invention are described further in thefollowing examples, which are illustrative and in no way limiting.

EXAMPLES

Experimental Procedures

Plasmids

EST clones containing human and mouse Sirt4 cDNA were obtained from theAmerican Type Culture Collection (Manassas, Va.). Human Sirt4 cDNA wasamplified by PCR with the oligonucleotides MHSirt4-3(5′-CACCGCGGTGGCGGCCGCATGAAGATGAGCTTTGCGTTGACTTTC-3′) (SEQ ID NO:4) andMHSirt4-4 (5′-CTTGTAATCCTCGAGGCATGGGTCTATCAAAGGCAGC-3′) (SEQ ID NO:5).The human Sirt4 cDNA fragment was digested at sites within theseoligonucleotide primers with NotI and XhoI, and the resulting fragmentwas inserted into the vector pCMV-FLAG-4A™ (Invitrogen; Carlsbad,Calif.) that had been digested with the same enzymes. The resultingplasmid, phSirt4FLAG, directs the overexpression of human Sirt4 with aC-terminal FLAG in mammalian cells. phSirt4 directs the overexpressionof human Sirt4 in mammalian cells and was created by amplification ofthe Sirt4 gene using the primers MHSirt4-3 and MHSirt4-QC2(5′.-CTTGTAATCCTCGAGTCAGCATGGGTCTATCAAAGGCAGC-3′) (SEQ ID NO:6). RNAiretroviral plasmids were constructed using pSUPER.retro™ as the backboneplasmid (OligoEngine, Seattle, Wash.). Mouse Sirt4 RNAi-a and -b wereconstructed by targeting the sequences 5′-CGCTTCCAAGCCCTGAACC-3′ (SEQ IDNO:7) and 5′-GGAGAGTTGCTGCCTTTAA-3′ (SEQ ID NO:8), respectively.

Cell Culture

HEK293T and HEPG2 cells were grown in DMEM medium supplemented withfetal bovine serum (FBS; 10% v/v), L-glutamine (2 mM), penicillin (100units/ml), and streptomycin (100 μg/ml). MIN6 cells were grown in DMEMmedium 1640, supplemented with FBS (15% v/v), L-glutamine (2 mM), sodiumbicarbonate (1 mM), β-mercaptoethanol (2.5 μl/500 ml), penicillin (100units/ml), and streptomycin (100 μg/ml). Cells were cultured at 37° C.in a humidified incubator containing 5% CO₂. All studies were performedusing asynchronous log-phase cultures, and MIN6 cells were used betweenpassages 29 and 40.

Viralproduction and Infections

The pBp-amphotrophic viruses were produced by cotransfection of 293T(Phoenix) cells with the pBABE™ and pSUPER™ constructs as described(Picard et al. (2004) Nature 429:771-6). Transfections were carried outusing jetPEI™ (Qbiogene, Carlsbad, Calif.). Virus was harvested 48 hourspost-transfection and added to MIN6 cells in the presence of polybrene(10 μg/ml). Eight hours after viral infection, fresh media was added.MIN6 cells were selected with puromycin (1 μg/mL) 48 h followinginfection.

Immunoprecipitation

Cells were harvested 48 h post-transfection by scraping into PBS andcentrifugation, and then incubated for 30 minutes in 3 ml of ice-coldNP40 lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1% NP40) containingprotease inhibitors (EDTA-free COMPLETE™; Roche Molecular Biochemicals,Indianapolis, Ind.), and dithiothreitol (1 mM DTT; Sigma, St. Louis,Mo.). The lysate was clarified by centrifugation for 15 min at 4° C. at14,000 rpm in a tabletop centrifuge, and the resulting supernatant wasincubated at 4° C. for 2 h with Protein A resin (Sigma) that had beenconjugated with anti-FLAG M2 (Sigma) or the appropriate antibody.Samples were washed four times with 10 ml of NP40 lysis buffer and thehSirt4-FLAG protein was eluted by the addition of FLAG peptide (400μg/ml, in 50 mM Tris pH 8.0, 150 mM NaCl, 10 mM DTT). Alternatively,protein complexes were eluted from the Protein A resin by adding proteinsample buffer (50 mM Tris-HCl (pH 6.8) containing 2% β-mercaptoethanol,2% SDS, 10% glycerol, 0.01% bromophenol blue), and then analyzed bySDS-PAGE and Western blotting.

Deacetylase Assay

Deacetylase activity of immunoprecipitated and dialyzed hSirt4-FLAG (50ng) was assessed by the FLUOR DE LYS™ kit according to themanufacturer's directions (BIOMOL Research Laboratories Inc., Pa.).hSirt1-FLAG was used as a positive control. Experiments were performedin the presence and absence of 1 mM NAD⁺.

ADP-ribosylation Assays

ADP-ribosylation activity was assessed as described in Tanny et al.(1999) Cell 99:735-45. Briefly, hSirt4-FLAG (50 ng), hSirt5-FLAG (50ng), or a buffer control were incubated with 3 μg histones and 3 μCi of³²P-NAD⁺ in 50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 10 mM DTT. The reactionmixture was incubated for 1 hour at 37° C., and the reaction stopped bythe addition of 90 μl ice-cold 22% trichloroacetic acid (TCA), incubatedon ice for 15 minutes, and centrifuged at 13,000 g for 15 minutes. Thepellets were resuspended and loaded onto 8.5% or 15% SDS polyacrylamidegels. After electrophoresis, gels were stained with Coomassie brilliantblue and ³²P in the gel detected by autoradiography.

Western Blots

Cells were lysed in protein sample buffer, vortexed, boiled for 5minutes, and centrifuged at 17,000×g for 5 minutes. Extractscorresponding to equivalent cell numbers (or 5-15 μg protein) weresubjected to SDS-PAGE (4-15% gradient) according to the method ofLaemmli ((1970) Nature 227:680-685), and transferred onto nitrocellulosemembranes and incubated for 60 minutes with blocking solution (3% lowfatmilk, 0.1% TWEEN®-20 in PBS). Membranes were incubated for 1 hour withappropriate primary antibodies. The anti-mono-ADP-ribose antibody was asdescribed (Meyer et al. (1986) Eur J Biochem 155:157-65). After 3-10minute washes in blocking buffer, membranes were incubated with theappropriate horseradish peroxidase-conjugated antibody (1:10,000). Thechemilumiiiescent signal was generated by incubation with the ECLreagent (Amersham Biosciences, Piscataway, N.J.).

Fluorescence Microscopy

HepG2 cells were grown on coverslips and transfected with phSirt4FLAGand pDSRed™2-Mito (BD Biosciences, Palo Alto, Calif.) 48 hours beforethe experiment. On the day of the experiment, cells were washed twicewith ice-cold PBS and then incubated in paraformaldehyde (4% w/v) atroom temperature for 10 minutes. The fixed cells were washed three timeswith PBS and then incubated in TRITON® X-100 (0.5% v/v) for 10 min andthen washed with PBS. The coverslips were mounted with VECTASHIELD®mounting media containing 4′,6-diamidino-2-phenyindole, dilactate (DAPI;Vector, Burlingame, Calif.). Fluorescence was visualized by using aconfocal microscope (Zeiss LSM510; Zeiss, Thomwood, N.Y.).

Immunohistochemistry of Mouse Tissues

Immunohistochemistry of endogenous Sirt4 in mouse tissue was performedusing a microwave citrate unmasking protocol. Briefly, mouse organsections were deparaffinized in xylene and rehydrated through an ethanolseries. Slides were then placed in citrate buffer (10 mM citric acid and25 mM NaOH) and microwaved on high power for 25 minutes. Slides werethen cooled in running tap water and soaked in PBS+0.1% Tween®-20 for 10minutes at room temperature. Slides were incubated in 10% donkey serumfor 1 hour at room temperature to block non-specific antibody binding.After 1 hour, primary antibody (1:100) was added, and slides wereincubated overnight at 4° C. in a humidified chamber. A primary antibodyagainst mouse Sirt4 was produced in a rabbit against the peptideLEMNFPLSSAAQDP (SEQ ID NO:9), which is in the C-terminal region of theprotein. Slides were then washed three times in PBS+0.1% TWEEN®-20 atroom temperature for 10 minutes each. Secondary antibody (1:200) wasadded, and the slides were incubated for 1 hour at 37° C. Slides werethen washed three times in PBS+0.1% TWEEN®-20 at room temperature,counterstained with DAPI, and coverslipped. Mouse monoclonal antibodyfor detection of insulin was obtained from Zymed Laboratories (SanFrancisco, Calif.). Secoridary antibodies were obtained from MolecularProbes (Eugene, Oreg.): ALEXA FLUOR®488 donkey α-mouse IgG and ALEXAFLUOR®594 donkey α-rabbit IgG. Images were acquired using a SPOT™digital camera (Diagnostic Instruments, Inc, Sterling Heights, Mich.)mounted on a ECLIPSE E600™ fluorescence microscope (Nikon).

Purification of Mitochondria

Mitochondria and other subcellular fractions were purified bydifferential centrifugation as described (Schwer et al. (2002) J CellBiol 158:647-57). Briefly, cells were collected in SEM, (150 mM NaCl, 10mM KCl, 10 mM Tris/HCl, pH 6.7), and then disrupted by a Douncehomogenizer. Samples were centrifuged twice at 1,000×g for 5 min topellet the nuclei and intact cells. To separate the mitochondrialfraction from the cytosolic fraction, we centrifuged the supernatant at5,000×g for 10 min. We washed the resulting pellet with sucrose/Mg²⁺medium (10 mM Tris/HCl, pH 6.7, 250 mM sucrose, 150 mM MgCl₂,),recentrifuged, and resuspended the final pellet in mitochondrialsuspension medium (10 mM Tris/HCl, pH 7.0, 250 mM sucrose). 10 μg ofprotein from each fraction was separated by SDS-PAGE and then analyzedby western blot.

Insulin Secretion Assays

MIN6 cells were plated in the wells of a 12-well plate at least 24 hoursbefore secretion assays. Cells were washed once with Krebs-Ringer-HEPESbuffer (KRB) containing 128 mMNaCl, 5 mM KCl, 2.7 mM CaCl₂, 1.2 mMMgSO₄, 1 mM Na₂HPO₄, 20 mM HEPES (pH 7.4). After incubation for 1-3hours in KRB containing 3 mM glucose, the cells were incubated in KRBcontaining either 3 or 16.7 mM glucose at 37° C. for one hour. Insulinconcentration was measured by ELISA (Alpco Diagnostics; Windham, N.H.).

Glutamate Dehydrogenase Assay

Glutamate dehydrogenase (50 μg; Ultrapure from Sigma) was incubated withor without Sirt4 (10 ng) in 200 μg of ADP-ribosylation buffer (50 mMTris pH 8.0, 10 mM DTT, 150 mM NaCl) in the presence or absence of 1 mMNAD or 1 mM nicotinamide at 37° C. for the indicated times. Then, analiquot of the reaction was assayed for glutamate dehydrogenaseactivity. Activity assays were performed at 25° C. using a BioSpec-1601spectrophotometer (Shimadzu Scientific Instruments, Inc; Braintree,Mass.) at A₃₄₀ based on the oxidation of NADH as described previously.Data was collected for 5-10 minutes at 10 second intervals. At the endof each experiment, less than 10% of substrates had been depleted.

Example 1 Purification and Enzymatic Activity of Sirt4

This example demonstrates that Sirt4 possesses an ADP-ribosyltransferaseactivity.

To investigate the enzymatic activity of hSirt4, two constructs weredesigned (phSirt4FLAG, phSirt4) to overproduce human Sirt4 with orwithout a C-terminal FLAG tag in mammalian cells. When 293T cells weretransfected with phSirt4FLAG, a 34 kDa band was produced that wasrecognized by both anti-FLAG and anti-hSirt4 antibodies (FIG. 1A). TheFLAG-tagged protein migrated more slowly than did the native version ofSirt4.

The enzymatic activity of Sirt4-FLAG protein immunoprecipitated frommammalian cells in a nondenaturing buffer was evaluated. Sirt4 was ableto transfer a radioactive ADP-ribosyl group from NAD to histones (FIG.1C). This ADP-ribosylation activity was inhibited by 1 mM nicotinamide(FIG. 1C). Mass spectroscopy confirmed that Sirt4 transferred anapproximately 500 Dalton moiety to Histone 2A. The molecular weight ofthis moiety corresponds to the molecular weight of ADP-ribose (FIG. 1D).

Example 2 Subcellular Localization of Sirt4

This example demonstrates that Sirt4 is localized to mitochondria.

Mammalian homologs of Sir2 have been localized to the nucleus (Luo etal. (2001) Cell 107:137-48; Vaziri et al. (2001) Cell 107:149-59),cytosol (North et al. (2003) Mol Cell 11:437-44), and mitochondria(Onyango et al. (2002) Proc Natl Acad Sci USA 99:13653-8; Schwer et al.(2002) J Cell Biol 158:647-57). To determine the localization of Sirt4,a plasmid was constructed (phSirt4GFP) that fused the C-terminus ofhuman Sirt4 with GFP (Sirt4-GFP). When HepG2 cells were transientlytransfected with phSirt4GFP, a punctate staining pattern was observed(FIG. 2A). Cotransfection experiments were performed with plasmids thattarget DSRed 2 to the mitochondria (pDSRed™2-Mito) or peroxisome(pDSRed™2-Peroxi). Sirt4-GFP colocalized with DSRed™2 that was targetedto the mitochondria (FIG. 2A), but did not colocalize with theperoxisomal DSRed™ marker. Transfections with GFP alone (i.e., GFP thatis not fused to Sirt4) did not result in a distinct localization pattern(FIG. 2B).

The mitochondrial localization of Sirt4 was verified by subcellularfractionation. Sirt4-FLAG was detected in the cell extract, wholecell/nucleus, and mitochondrial fractions, but not in thecytosolic/light fraction (FIG. 2C). HSP60, a mitochondrial marker, alsoco-fractionated with Sirt4-FLAG, while catalase could be detectedstrongly in the cytosolic/light fraction, but not in the mitochondrialfraction (FIG. 2C). In separate experiments, endogenous Sirt4 wasdetected in the mitochondrial fraction of both 293T and mouse MIN6cells. These results strongly suggest that Sirt4 is localized to themitochondria of human and mouse cells.

The N-terminus of Sirt4-FLAG was analyzed by Edman degradation todetermine whether Sirt4 is post-translationally cleaved duringmitochondrial import. As depicted in FIG. 2D, the first 28 amino acidresidues were absent from the N-terminus, indicating that the proteinhad been post-translationally processed. In addition, a Sirt4-FLAGconstruct lacking the first 28 amino acids was not stable in cells.Thus, Sirt4 is post-translationally processed, likely by cleavage afterserine 28, upon targeting to the mitochondria.

Example 3 Expression of Sirt4 in Mouse Tissues

This example demonstrates the distribution of Sirt4 in mouse tissues.

To understand the biological function of Sirt4, its endogenousexpression profile in mouse tissues was determined byimmunohistochemistry using antibodies generated against the C-terminusof mouse Sirt4. High levels of staining were observed in neurons andpancreatic islets. Moderate staining was observed in muscle, heart,liver, and kidney, and testes. Sirt4 was expressed strongly in islets ofthe pancreas, but not in surrounding goblet or acinar cells (FIG. 3A andB). The expression of Sirt4 overlapped with the expression of insulinwithin islets (FIG. 3), indicating that Sirt4 may be involved in normalβ-cell function.

Example 4 Sirt4 Regulates the Production and Secretion of Insulin

To test the role of Sirt4 in β-cell biology, insulin secretion in themouse insulinoma, MIN6, β-cell line was studied. Using two separate RNAiconstructs, stable MIN6 cells that had decreased levels of Sirt4 whencompared to control cells that were infected with the empty vector as acontrol were engineered (FIG. 4A). To study insulin secretion, thesecells were incubated in KRB containing 3 mM glucose, and then shifted toKRB containing either 3 (low) or 16.7 mM (high) glucose. Sirt4 RNAitreated cells secreted 2-fold more insulin when compared to controlcells at both low and high glucose concentrations (FIG. 4B). The Sirt4RNAi treated cells maintained a normal ability to respond to glucose, asthe Sirt4 RNAi-expressing cells still responded to 16.7 mM glucose bysecreting proportional insulin. Thus, the magnitude of insulin secretiondiffered between normal and Sirt4 RNAi cells, and this difference wasmaintained at difference glucose levels. The intracellular insulin levelwas determined at low and high glucose concentrations, and the Sirt4RNAi treated cells were found to contain 2-fold higher levels of insulin(FIG. 4C).

Example 5 Sirt4 Interacts With Mitochondrial Proteins

To identify transient, yet biochemically relevant interactions,ADP-ribosylation within the mitochondria was investigated. Isolatedmitochondria were incubated with [³²P]-NAD to identify ADP-ribosylatedmitochondrial proteins. In agreement with previous studies (Ziegler(2000) Eur J Biochem 267:1550-64), three predominant modified proteinswere observed (FIG. 5A), one of which has been identified as glutamatedehydrogenase (GDH) (Herrero-Yraola et al. (2001) EMBO J 20:2404-12).Anti-glutamate dehydrogenase immunoprecipitated a 55 kDa-radioactiveprotein (FIG. 5B). By contrast, immunoprecipitation by antibodiesagainst hSirt4 or the prevalent mitochondrial protein, ANT1 did not givea significant radioactive band that migrated at 55 kDa.

The interaction between Sirt4 and mitochondrial proteins in 293T cellsthat overexpressed hSirt4-FLAG was investigated. Immunoprecipitationsusing α-FLAG antibodies isolated a complex between Sirt4-FLAG andglutamate dehydrogenase (GDH), insulin degrading enzyme (IDE), andadenine nucleotide transporter (ANT) in Sirt4 overexpressing cells, butnot control cells (FIG. 5C). The complex between Sirt4-FLAG and GDH wasalso be identified by immunoprecipitation with α-glutamate dehydrogenaseantibodies (FIG. 5C).

MIN6 cells were used to investigate the endogenous interaction betweenSirt4 and GDH, IDE, and ANT. Sirt4 was immunoprecipitated from MIN6cells using the C-terminal antibody, and the blots were probed withantibodies against GDH, IDE, and ANT. Sirt4 was able to form anendogenous complex with glutamate dehydrogenase (FIG. 5D), insulindegrading enzyme, and adenine nucleotide transporter in MIN6 cells.These results indicate that Sirt4 can form a complex with each of GDH,IDE, and ANT under physiological protein concentrations.

Mitochondria from 293T control or Sirt4-FLAG overexpressing cells wereincubated with [³²P]-NAD, and the ADP-ribosylation state of glutamatedehydrogenase was measured by immunoprecipitation and subsequentautoradiography. Sirt4 overexpression enhanced the ADP-ribosylation ofglutamate dehydrogenase (FIG. 5E). Moreover, a small amount of labeledglutamate dehydrogenase could be detected in a complex with Sirt4 (FIG.5E).

It is believed that the Sirt4 may act in β-cells to control insulinlevels by interactions with all of GDH, ANT, and IDE.

Example 6 Sirt4 Inhibits Glutamate Dehydrogenase Activity

Sirt4 or a buffer control was incubated with bovine recombinantglutamate dehydrogenase for one hour in the presence of NAD. Then, theglutamate dehydrogenase activity was assessed by monitoring thedisappearance of NADH (A₃₄₀). Sirt4, but not the buffer control,significantly reduced the enzymatic activity of glutamate dehydrogenase.To verify that this inhibition was dependent on the availability ofNAD⁺, we incubated Sirt4 with or without NAD⁺ with glutamatedehydrogenase for various times. Sirt4 inhibited glutamate dehydrogenaseactivity only in the presence of NAD⁺ (FIG. 6B), and within 2 hours theactivity of glutamate dehydrogenase was inhibited by 50%. Afterincubating for 12 hours, the activity of glutamate dehydrogenase wasinhibited by more than 90%.

MIN6 cells were co-infected with RNAi plasmids targeting Sirt4 andglutamate dehydrogenase. Co-infected cells contained less insulin thandid Sirt4-RNAi cells (FIG. 7A), indicating that elevated glutamatedehydrogenase activity could account for the increase in insulinsecreted. To test further whether glutamate dehydrogenase activity wasaltered in Sirt4 RNAi cells, insulin secretion assays were performed inthe presence and absence of a glutamate dehydrogenase activator, BCH,which is known to stimulate insulin secretion. Control cells that werestimulated with both BCH and 16.7 mM glucose demonstrated enhancedinsulin secretion when compared to cells stimulated with 16.7 mM glucosealone (FIG. 7B). Sirt4 RNAi treated cells did not secrete more insulinwhen incubated with BCH and 16.7 mM glucose when compared to the 16.7 mMglucose condition, indicating that glutamate dehydrogenase activity maybe already elevated in these cells. Finally, the activity of glutamatedehydrogenase from purified mitochondria isolated from normal or Sirt4RNAi treated cells was measured. A 20% increase in the enzymaticactivity of glutamate dehydrogenase in the Sirt4 RNAi treated cells wasfound (FIG. 7C). Taken together, these data show that a decrease in thelevels of Sirt4 leads to a functional gain in glutamate dehydrogenaseactivity.

Example 7 Sirt4 Function in β-cell Energetics

To explore the mechanism of how Sirt4 and glutamate dehydrogenaseregulate insulin secretion from pancreatic β-cells, two parametersregulated by the mitochondria and change upon glucose stimulation weremeasured: ATP concentration and oxygen consumption. As expected, controlcells showed an increase in ATP content when shifted from 3 to 16.7 mMglucose (FIG. 8A). Sirt4 RNAi treated cells demonstrated a significantincrease in ATP content in both 3 and 16.7 mM glucose concentrations, ascompared to control cells. These cells still produced more ATP whenstimulated with 16.7 mM glucose, indicating that their glucosemetabolism was intact.

Oxygen consumption is another measure of the cell's metabolic state andwill increase with glucose stimulation. The reduction of Sirt4 levelscaused cells to consume 2-fold more oxygen in 16.7 mM glucose than thecontrol cells (FIG. 8B). As both ATP level and rate of oxygenconsumption increased in Sirt4-RNAi cells, their metabolic rate isup-regulated in a coupled process.

Example 8 Determination of Putative Regulatory Sequences for SIRT4

To determine conserved putative transcription factor binding sitesinvolved in the regulation of Sirt4, genomic sequences 5 kb upstream ofthe start of the first codon of human and mouse Sirt4 were input to therVISTA™ program (Loots et al. (2002) Genome. Res. 12:832-839). Theoutput of the program is shown in FIG. 9.

All patents, patent applications, and references cited herein are herebyincorporated by reference in their entirety. Other embodiments arewithin the scope of the following claims.

1. A method of evaluating Sirt4 activity, the method comprising:providing a cell-free composition that comprises a Sirt4 protein, anADP-ribosyl donor, and a substrate; and evaluating ADP-ribosylationactivity in the composition.
 2. The method of claim 1, wherein theADP-ribosyl donor comprises NAD.
 3. The method of claim 2, wherein theNAD is radio-labeled.
 4. The method of claim 1, wherein the substratecomprises a peptide.
 5. The method of claim 1, wherein the substratecomprises GDH, aldehyde dehydrogenase, or histones, or a fragment of anythereof.
 6. The method of claim 1, wherein the providing comprisescombining a preparation of the Sirt4 protein that is at least 10% purewith the ADP-ribosyl donor and the substrate.
 7. The method of claim 1,wherein the Sirt4 protein comprises a sequence at least 85% identical toSEQ ID NO:3.
 8. The method of claim 1, wherein the Sirt4 proteincomprises a sequence at least 85% identical to SEQ ID NO:1 or amino acidresidues 29-314, 29-308, 30-314, 36-308, 42-308, 42-300, or 56-314 ofSEQ ID NO:1.
 9. The method of claim 1, further comprising including atest compound in the cell-free composition.
 10. A method of evaluatingthe effect of a test compound on Sirt4, the method comprising: a)providing a reaction mixture comprising Sirt4 and a test compound; andb) evaluating an activity of Sirt4.
 11. The method of claim 10, whereinthe activity is ADP-ribosyltransferase activity.
 12. The method of claim10, wherein the reaction mixture comprises NAD or an NAD analog.
 13. Themethod of claim 10, wherein the NAD or NAD analog comprises aradioactive label.
 14. The method of claim 10, wherein the reactionmixture comprises an ADP-ribosylation substrate selected from the groupconsisting of: GDH, aldehyde dehydrogenase, and histones.
 15. The methodof claim 10, wherein the test compound is a small molecule.
 16. Themethod of claim 10, wherein the method is repeated for each of aplurality of test compounds from a chemical library.
 17. The method ofclaim 10, wherein the Sirt4 comprises a sequence at least 85% identicalto SEQ ID NO:3.
 18. The method of claim 10, wherein the Sirt4 comprisesa sequence at least 85% identical to SEQ ID NO:1 or amino acid residues29-314, 29-308, 30-314, 36-308, 42-308, 42-300, or 56-314 of SEQ IDNO:
 1. 19. The method of claim 10, further comprising c) comparing theactivity evaluated in (b) with the Sirt4 activity evaluated in theabsence of the test compound.
 20. A method of identifying a compoundthat alters a Sirt4-associated parameter in a cell, the methodcomprising: a) contacting a test compound to a cell that expressesSirt4; and b) evaluating a Sirt4-associated parameter associated withthe cell.
 21. The method of claim 20, wherein the Sirt4-associatedparameter is ADP-ribosylation activity.
 22. The method of claim 20,wherein the test compound is a small molecule.
 23. The method of claim20, wherein the method is repeated for each of a plurality of testcompounds from a chemical library.
 24. The method of claim 20, furthercomprising c) comparing the parameter determined in (b) with aSirt4-associated parameter evaluated in the absence of the testcompound.
 25. A method of modulating insulin secretion in response toglucose, the method comprising modulating the expression or activity ofSirt4 in an insulin-secreting cell.
 26. The method of claim 25, whereininsulin secretion is increased by decreasing the expression or activityof Sirt4.
 27. The method of claim 25, wherein insulin secretion isdecreased by increasing the expression or activity of Sirt4.
 28. Themethod of claim 25, wherein insulin secretion is modulated in vitro. 29.The method of claim 25, wherein insulin secretion is modulated in asubject.
 30. The method of claim 25, wherein the modulation of Sirt4expression or activity is effected by administering an agent thatmodulates Sirt4 expression or activity.
 31. A method of treating orpreventing a metabolic disorder, the method comprising administering, toa subject, an agent that modulates the expression or activity of Sirt4,in an amount effective to treat or prevent the metabolic disorder. 32.The method of claim 31, wherein the metabolic disorder is diabetes,insulin resistance, metabolic syndrome, or pre-diabetes.
 33. The methodof claim 31, wherein the levels of Sirt4 are modulated in aninsulin-secreting cell.
 34. The method of claim 31, wherein the agent isan antagonistic nucleic acid that reduces Sirt4 expression.
 35. Themethod of claim 31, wherein the agent comprises an siRNA that targetsSirt4 mRNA.
 36. A method of treating or preventing a symptom of aneurodegenerative disorder, the method comprising administering to asubject a compound that increases the expression or activity of Sirt4 inan amount effective to treat or prevent the neurodegenerative disorder.37. The method of claim 36, wherein the neurodegenerative disorderinvolves accumulation of β-amyloid peptide.
 38. The method of claim 36,wherein the neurodegenerative disorder is Alzheimer's disease.